{"anonymous_execution":false,"authentication_required_for_execution":true,"links":{"agent_skill":"/SKILL.md","mcp":"/mcp","models":"/models.json","openapi":"/api/openapi.json"},"schema":"ubi.tools-catalog/v1","source_digest":"a079441cd3eb2694a95855648de9cb25ba306ae4db3f7fb91423d7a6abb0d66e","tools":[{"display_name":"AbLang2","license":"BSD-3-Clause","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"ablang2.embed_antibody_sequences","description":"Create one checksum-verified 480-dimensional float64 sequence-level representation for each valid heavy, light, or paired antibody variable-domain row.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"ablang2.embed_antibody_sequences","parameters":{"heavy_chain_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing a configurable heavy-chain column, light-chain column, or paired heavy/light columns.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"sequences","title":"Antibody variable-domain sequences"}],"limits":{"embedding_dimension":480,"max_native_batch_size":1,"max_native_sequence_length":512,"max_paired_residues":360,"max_rows_per_job":1,"max_total_residues":2880,"max_variable_domain_length":180,"min_rows_per_job":1,"min_variable_domain_length":40,"supported_alphabet":"unambiguous_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Create antibody sequence embeddings with AbLang2","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing source fields, structured row status, one exact 480-dimensional float64 sequence-level representation per valid row, binary-vector digest, model bundle digest, and native result digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"sequence_embeddings","title":"AbLang2 antibody sequence embeddings"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified AbLang2 embedding response containing the complete vectors, signed work units, row order, and qualification evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AbLang2 embedding result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_chain_column":{"default":"sequence","description":"Optional Dataset column containing heavy-chain variable-domain sequences. Null enables light-only analysis when a light-chain column is supplied.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy-chain column","type":["string","null"]},"light_chain_column":{"default":null,"description":"Optional Dataset column containing light-chain variable-domain sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Light-chain column","type":["string","null"]}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"ablang2.propose_mutation_preferences","description":"Rank chain-aware candidate substitutions by AbLang2 model log-probability ratio to the source residue using corrected tokenizer indices and one-based within-chain positions.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"ablang2.propose_mutation_preferences","parameters":{"heavy_chain_column":"sequence","top_k":10},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing configurable heavy, light, or paired variable-domain columns without masks.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"sequences","title":"Antibody sequences for substitution review"}],"limits":{"candidate_substitutions_per_residue":19,"max_native_batch_size":1,"max_native_sequence_length":512,"max_paired_residues":360,"max_returned_proposals":100,"max_rows_per_job":1,"max_total_residues":360,"max_variable_domain_length":180,"min_rows_per_job":1,"min_variable_domain_length":40,"supported_alphabet":"unambiguous_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Rank antibody mutation preferences with AbLang2","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing chain-aware one-based substitutions, source and proposed probabilities, model log-probability ratios, stable ranks, model bundle digest, and native result digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"mutation_preferences","title":"AbLang2 mutation-preference ranking"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified AbLang2 stepwise-masking response, including signed work units and the explicit model-preference interpretation boundary.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AbLang2 mutation-preference result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_chain_column":{"default":"sequence","description":"Optional Dataset column containing heavy-chain variable-domain sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy-chain column","type":["string","null"]},"light_chain_column":{"default":null,"description":"Optional Dataset column containing light-chain variable-domain sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Light-chain column","type":["string","null"]},"top_k":{"default":10,"description":"Maximum number of chain-aware substitutions returned after stable model-preference ranking.","maximum":100,"minimum":1,"title":"Mutation preferences to return","type":"integer"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":8,"max_rows_per_native_batch":8,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"ablang2.restore_masked_residues","description":"Restore only explicit '*' masks in heavy, light, or paired variable domains while preserving chain lengths and every unmasked residue, with complete canonical-amino-acid probabilities.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"ablang2.restore_masked_residues","parameters":{"heavy_chain_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing one or more '*' masks in configurable heavy, light, or paired variable-domain columns.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"sequences","title":"Explicitly masked antibody sequences"}],"limits":{"max_masks_per_record":16,"max_native_batch_size":8,"max_native_sequence_length":512,"max_paired_residues":360,"max_rows_per_job":8,"max_total_masks":64,"max_total_residues":1440,"max_variable_domain_length":180,"min_rows_per_job":1,"min_variable_domain_length":40,"supported_alphabet":"canonical_protein_plus_explicit_star_mask"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Restore explicit antibody residue masks with AbLang2","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing original and restored chain sequences, explicit one-based mask positions, selected residues, complete canonical-amino-acid probabilities, model bundle digest, and native result digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"restored_sequences","title":"AbLang2-restored antibody sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified AbLang2 restoration response proving that chain lengths and every unmasked residue were preserved.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AbLang2 restoration result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_chain_column":{"default":"sequence","description":"Optional Dataset column containing heavy-chain sequences with explicit '*' masks.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Masked heavy-chain column","type":["string","null"]},"light_chain_column":{"default":null,"description":"Optional Dataset column containing light-chain sequences with explicit '*' masks.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Masked light-chain column","type":["string","null"]}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":100,"max_rows_per_native_batch":100,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"ablang2.score_antibody_sequences","description":"Calculate exact AbLang2 confidence or pseudo-log-likelihood scores for antibody heavy chains and optional paired light chains using the checksum-bound ABLANG-2-paired model bundle.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"ablang2.score_antibody_sequences","parameters":{"heavy_chain_column":"sequence","score_type":"confidence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing antibody heavy-chain sequences and, optionally, paired light-chain sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Antibody sequences"}],"limits":{"max_native_batch_size":100,"max_rows_per_job":100,"max_sequence_length":500,"max_total_residues":100000,"min_rows_per_job":1,"min_variable_domain_length":40,"supported_alphabet":"unambiguous_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score antibody sequences with AbLang2","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing source fields, structured row status, exact AbLang2 score, pseudo-perplexity, scoring mode, model bundle digest, and native result digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"scored_sequences","title":"AbLang2-scored antibody sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified AbLang2 request result used for conformance, provenance, and reproducibility.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AbLang2 result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_chain_column":{"default":"sequence","description":"Dataset column containing the antibody heavy-chain amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy-chain column","type":"string"},"light_chain_column":{"default":null,"description":"Optional dataset column containing the paired light-chain amino-acid sequence. Null scores heavy chains alone.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Light-chain column","type":["string","null"]},"score_type":{"default":"confidence","description":"Confidence performs one forward pass; pseudo-log-likelihood performs masked-residue scoring and is substantially slower.","enum":["confidence","pseudo_log_likelihood"],"title":"Score type","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://github.com/oxpig/AbLang2","tool_id":"ablang2","version":"0.2.1"},{"display_name":"abmpnn","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":2,"max_rows_per_native_batch":2,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"abmpnn.design_antibody_sequences","description":"Generate structure-conditioned antibody heavy-chain or paired heavy/light-chain sequence candidates with explicit antibody chain roles, fixed antibody positions, deterministic sampling, and the checksum-qualified official AbMPNN fine-tuned checkpoint.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"abmpnn.design_antibody_sequences","parameters":{"backbone_noise_angstrom":0.0,"fixed_positions":{},"heavy_chain_id":"<heavy_chain_id>","num_sequences":4,"omit_amino_acids":[],"sampling_temperature":0.1,"seed":42},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version containing checksum-bound full-backbone PDB Artifacts and explicit one-character heavy and optional light chain IDs.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Antibody structures"}],"limits":{"max_native_batch_size":2,"max_pdb_bytes_per_job":4194304,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":2,"max_sequences_per_structure":16,"max_total_residues":2000,"min_rows_per_job":1,"optional_antibody_chain_roles":["light_chain_id"],"required_antibody_chain_roles":["heavy_chain_id"],"supported_alphabet":"unambiguous_protein","supported_structure_media_type":"chemical/x-pdb"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design antibody sequences with AbMPNN","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable row-preserving Dataset retaining the source antibody structure, explicit heavy/light design roles, context chains, exact candidate sequences and mutations, fixed-position compliance, scores, parameters, checkpoint/source digests, row status, and lineage. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_antibody_sequences","title":"AbMPNN antibody sequence designs"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified AbMPNN response containing exact PDB, antibody chain roles, context chains, samples, mutations, fixed positions, official checkpoint identity, source, request, row, batch, and measured execution evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AbMPNN result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"backbone_noise_angstrom":{"default":0.0,"maximum":1.0,"minimum":0.0,"title":"Backbone noise","type":"number"},"fixed_positions":{"additionalProperties":{"items":{"minimum":1,"type":"integer"},"minItems":1,"type":"array","uniqueItems":true},"default":{},"description":"Per-chain sorted unique one-based sequence positions to preserve on the declared heavy or light chain.","propertyNames":{"pattern":"^[A-Za-z0-9]$"},"title":"Fixed antibody positions","type":"object"},"heavy_chain_id":{"description":"Required one-character PDB heavy-chain ID to redesign.","pattern":"^[A-Za-z0-9]$","title":"Heavy chain","type":"string"},"light_chain_id":{"default":null,"description":"Optional one-character PDB light-chain ID to redesign. Null leaves every non-heavy chain fixed.","pattern":"^[A-Za-z0-9]$","title":"Light chain","type":["string","null"]},"num_sequences":{"default":4,"maximum":16,"minimum":1,"title":"Sequences per structure","type":"integer"},"omit_amino_acids":{"default":[],"description":"Sorted unique canonical amino acids excluded from sampling.","items":{"enum":["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"],"type":"string"},"maxItems":19,"title":"Omitted amino acids","type":"array","uniqueItems":true},"sampling_temperature":{"default":0.1,"maximum":1.0,"minimum":0.05,"title":"Sampling temperature","type":"number"},"seed":{"default":42,"description":"A positive base seed. Record i uses seed+i in stable input order.","maximum":2147483645,"minimum":1,"title":"Deterministic base seed","type":"integer"}},"required":["heavy_chain_id"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"abmpnn","version":null},{"display_name":"AbNumber","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"abnumber.number_sequences","description":"Number antibody variable-region sequences and annotate framework/CDR residues with AbNumber.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"abnumber.number_sequences","parameters":{"scheme":"imgt","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing protein sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Antibody sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":500,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Number antibody sequences","outputs":[{"content_schema":null,"dataset_kind":null,"description":"Complete scientist-facing numbered rows, CDR sequences, per-row failures, and the native AbNumber response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Numbered sequence results"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_type":{"default":null,"description":"Optional chain-type constraint; null enables automatic detection.","enum":["heavy","light",null],"examples":["heavy"],"title":"Chain type","type":["string","null"]},"scheme":{"default":"imgt","description":"Residue numbering scheme.","enum":["imgt","kabat","chothia","aho"],"examples":["imgt"],"title":"Numbering scheme","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing amino-acid sequences.","examples":["sequence"],"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/prihoda/AbNumber","tool_id":"abnumber","version":"0.4.4"},{"display_name":"abodybuilder3","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":10,"max_rows_per_native_batch":10,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"abodybuilder3.predict_antibody_structures","description":"Predict paired heavy/light antibody variable-domain structures with the official checksum-bound ABodyBuilder3 pLDDT-loss checkpoint and emit independently verified PDB coordinates and per-residue pLDDT evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"light_chain":"<value>","sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"abodybuilder3.predict_antibody_structures","parameters":{"heavy_chain_column":"sequence","light_chain_column":"light_chain"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing paired heavy- and light-chain variable-domain amino-acid sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence","light_chain"],"resource_kinds":["inline"],"role":"sequences","title":"Paired antibody sequences"}],"limits":{"max_native_batch_size":10,"max_pdb_bytes":2097152,"max_rows_per_job":10,"max_sequence_length":180,"max_total_residues":3600,"min_rows_per_job":1,"min_variable_domain_length":40,"supported_alphabet":"unambiguous_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict paired antibody structures with ABodyBuilder3","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Structures Dataset containing source chain sequences, structured row status, verified PDB artifacts, chain and residue counts, pLDDT summaries, model checkpoint digest, and native result digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"predicted_structures","title":"ABodyBuilder3 antibody structures"},{"content_schema":null,"dataset_kind":null,"description":"The immutable independently verified ABodyBuilder3 batch response containing exact PDB and per-residue pLDDT evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native ABodyBuilder3 result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_chain_column":{"default":"sequence","description":"Dataset column containing the antibody heavy-chain amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy-chain column","type":"string"},"light_chain_column":{"default":"light_chain","description":"Dataset column containing the paired antibody light-chain amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Light-chain column","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"abodybuilder3","version":null},{"display_name":"Aggrescan3D","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":4,"max_rows_per_native_batch":4,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"aggrescan3d.score_structures","description":"Calculate checksum-bound Aggrescan3D 1.1.0 static residue scores from immutable PDB structures with exact FreeSASA accessibility, surface and distance-neighborhood components, PDB residue identities, transparent positive-score regions, and independently reconstructable digests.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"aggrescan3d.score_structures","parameters":{"distance_angstrom":10},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version containing checksum-bound PDB Artifacts and their immutable structure evidence.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Protein structures"}],"limits":{"max_native_batch_size":4,"max_pdb_bytes_per_job":8388608,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":4,"maximum_distance_angstrom":30,"min_rows_per_job":1,"minimum_distance_angstrom":1,"supported_structure_media_type":"chemical/x-pdb"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score protein structures with Aggrescan3D","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Structures Dataset containing exact PDB residue identities, FreeSASA relative accessibility, independently reconstructed surface and distance-neighborhood components, A3D scores, positive-score regions, summary statistics, structured row status, and source/runtime/result digests. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"scored_structures","title":"Aggrescan3D-scored structures"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified Aggrescan3D static response containing exact PDB, chain, residue, source bundle, FreeSASA runtime, request, row, parameter, and batch evidence. Dynamic CABS-flex/Modeller and FoldX mutation modes are explicitly unavailable.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Aggrescan3D static result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_id":{"default":null,"description":"Optional one-character PDB chain identifier. Null scores every supported protein chain in structure order.","pattern":"^[A-Za-z0-9-]$","title":"PDB chain","type":["string","null"]},"distance_angstrom":{"default":10,"description":"CA-distance cutoff used by the exact Aggrescan3D neighborhood-weighting equation.","maximum":30,"minimum":1,"title":"Distance cutoff","type":"integer"},"ph":{"default":null,"description":"Optional pH-dependent Aggrescan3D residue scale. Null uses the canonical static score matrix.","exclusiveMinimum":0,"maximum":14,"title":"pH","type":["number","null"]}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://bitbucket.org/lcbio/aggrescan3d","tool_id":"aggrescan3d","version":"1.1.0"},{"display_name":"analytics","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":20000,"max_rows_per_native_batch":20000,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_collective","successful_items_preserved":false},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"analysis.check_synthesis_sequences","description":"Group complete design and synthesized sequences by declared name and publish full global alignments, coordinate-level edits, conflicts, and unverified states with deterministic evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"datasets"}],"capability_id":"analysis.check_synthesis_sequences","parameters":{"design_input_count":1,"molecule_type":"protein","name_case_sensitive":true,"name_column":"name","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","protein_sequences","annotated_sequences","alignment","comparison"],"description":"Two to twenty frozen Selections or immutable sequence Dataset Versions. The first design_input_count inputs are designs and the remaining inputs are synthesized sequences.","granularity":["selection","dataset_version"],"max_items":20,"media_types":[],"min_items":2,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"datasets","title":"Ordered design and synthesized sequence inputs"}],"limits":{"max_alignment_cells":20000000,"max_datasets_per_job":20,"max_rows_per_job":20000,"max_rows_per_native_batch":20000,"max_sequence_characters":20000000,"max_sequence_length":5000,"min_datasets_per_job":2,"min_rows_per_job":2,"supported_alphabets":["canonical_protein","iupac_nucleotide"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Check synthesized sequences against designs","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Every design and synthesized record with deterministic group status, full global alignment, coordinate-level mismatches, and explicit conflict or missing-counterpart evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"synthesis_check_dataset","title":"Synthesis Check comparison"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native grouping, alignment, mismatch, policy, and digest response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Synthesis Check evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"design_input_count":{"default":1,"description":"The first N ordered inputs are designs; at least one later synthesized input is required.","maximum":19,"minimum":1,"title":"Leading design input count","type":"integer"},"molecule_type":{"default":"protein","enum":["protein","nucleotide"],"title":"Molecule type","type":"string"},"name_case_sensitive":{"default":true,"title":"Case-sensitive name grouping","type":"boolean"},"name_column":{"default":"name","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence name column","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Full prepared sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"analysis.compare_cluster_abundance","description":"Compare ordered immutable samples by an explicit harmonized feature key with exact count conservation, normalization, baseline fold change, Fisher enrichment, and multiple-testing evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"cluster_representative_sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"samples"}],"capability_id":"analysis.compare_cluster_abundance","parameters":{"baseline_first":true,"feature_key_column":"cluster_representative_sequence","fold_change_pseudocount":0.5,"mode":"overview","normalization":"counts_per_million","representative_sequence_column":"cluster_representative_sequence","sample_labels":[],"valid_statuses":["CORRECT","VALID","PASS","SUCCESS","SUCCEEDED","OK"]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["clusters"],"description":"Two to twenty frozen Selections or immutable CLUSTERS Dataset Versions whose configured feature keys are already harmonized across samples.","granularity":["selection","dataset_version"],"max_items":20,"media_types":[],"min_items":2,"ordered":true,"required":true,"required_fields":["cluster_representative_sequence"],"resource_kinds":["inline"],"role":"samples","title":"Ordered cluster samples"}],"limits":{"max_enrichment_tests":50000,"max_features_per_job":5000,"max_fisher_support_points":5000000,"max_rows_per_job":1,"max_samples_per_job":20,"max_total_count":1000000,"min_samples_per_job":2},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Compare cluster abundance","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"One exact harmonized-feature row with grouped sample abundance, normalization, fold-change, quality, and enrichment evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"cluster_comparison","title":"Multi-sample cluster comparison"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native comparison response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native comparison evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"baseline_first":{"default":true,"type":"boolean"},"baseline_ordinal":{"default":null,"maximum":19,"minimum":0,"title":"Zero-based baseline input ordinal","type":["integer","null"]},"feature_key_column":{"default":"cluster_representative_sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Harmonized feature key column","type":"string"},"fold_change_pseudocount":{"default":0.5,"maximum":1000000,"minimum":0,"type":"number"},"mode":{"default":"overview","enum":["overview","baseline_fold_change","fisher_enrichment"],"type":"string"},"normalization":{"default":"counts_per_million","enum":["raw_count","fraction","counts_per_million"],"type":"string"},"quality_score_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional quality score column","type":["string","null"]},"representative_sequence_column":{"default":"cluster_representative_sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Representative protein sequence column","type":["string","null"]},"row_status_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional validity status column","type":["string","null"]},"sample_labels":{"default":[],"items":{"maxLength":200,"minLength":1,"type":"string"},"maxItems":20,"title":"Optional labels in input order","type":"array"},"valid_statuses":{"default":["CORRECT","VALID","PASS","SUCCESS","SUCCEEDED","OK"],"items":{"maxLength":100,"minLength":1,"type":"string"},"maxItems":20,"minItems":1,"title":"Included statuses","type":"array","uniqueItems":true}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"analysis.compare_reference_sequences","description":"Globally align bounded immutable candidates against an exact approved Reference Library Version and return reproducible similarity evidence and human-review flags without legal conclusions.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"candidates"},{"resource_id":"<immutable-resource-id>","resource_kind":"reference","role":"references"}],"capability_id":"analysis.compare_reference_sequences","parameters":{"alignment_method":"global_unit_edit","label_column":"candidate_label","molecule_type":"<molecule_type>","review_identity_threshold":0.8,"sequence_column":"sequence","top_match_count":5},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","nucleotide_sequences","annotated_sequences"],"description":"One frozen Selection or immutable sequence Dataset Version containing up to 25 protein or nucleotide candidates.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"candidates","title":"Candidate sequences"},{"dataset_kinds":[],"description":"One exact, checksum-bound, approved organization-supplied or licensed Reference Library Version.","granularity":["reference_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["reference"],"role":"references","title":"Approved Reference Library Version"}],"limits":{"max_alignment_cells":20000000,"max_references_per_job":250,"max_rows_per_job":1,"max_sequence_length":2000,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Compare sequences to an approved Reference Library","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Ranked exact global-alignment evidence and non-legal human-review flags for every candidate against one approved immutable Reference Library Version. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"reference_similarity","title":"Reference similarity evidence"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native similarity response with exact library, index, provenance, and algorithm digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native reference-review evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"alignment_method":{"default":"global_unit_edit","enum":["global_unit_edit"],"title":"Alignment method","type":"string"},"label_column":{"default":"candidate_label","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional candidate label column","type":["string","null"]},"molecule_type":{"enum":["protein","nucleotide"],"title":"Molecule type","type":"string"},"review_identity_threshold":{"default":0.8,"maximum":1.0,"minimum":0.0,"title":"Human-review identity threshold","type":"number"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Candidate sequence column","type":"string"},"top_match_count":{"default":5,"maximum":10,"minimum":1,"title":"Top matches per candidate","type":"integer"}},"required":["molecule_type"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"analysis.detect_mixed_wells","description":"Detect complete translated heavy- or light-chain identities shared across canonical plate wells, retaining invalid rows and exact source alignment evidence without making a contamination diagnosis.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"records"}],"capability_id":"analysis.detect_mixed_wells","parameters":{"chain_column":"chain","heavy_chain_values":["IGH","IGG-H","VH","H","HEAVY"],"light_chain_values":["IGK","IGL","IGG-L","VK","VL","K","L","LIGHT"],"plate_format":96,"reading_frame":1,"sequence_column":"sequence","sequence_type":"nucleotide","well_column":"well"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","protein_sequences","annotated_sequences","alignment","comparison"],"description":"One frozen Selection or immutable sequence Dataset Version with explicit sequence, chain label, and canonical well fields.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"records","title":"Plate sequence records"}],"limits":{"max_rows_per_job":1,"max_sequence_characters":20000000,"max_sequence_length":5000,"min_rows_per_job":1,"supported_alphabets":["canonical_protein","unambiguous_coding_dna"],"supported_plate_formats":[96,384]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Detect exact mixed-well sequence identities","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Every source row with exact translated chain identity, canonical plate/well status, all matched records, and complete source-alignment evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"mixed_well_dataset","title":"Mixed-well identity evidence"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native identity groups, plate summaries, translations, invalid rows, policies, and digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native mixed-well evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_column":{"default":"chain","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Chain label column","type":"string"},"heavy_chain_values":{"default":["IGH","IGG-H","VH","H","HEAVY"],"items":{"maxLength":100,"minLength":1,"type":"string"},"maxItems":20,"minItems":1,"title":"Heavy-chain labels","type":"array","uniqueItems":true},"light_chain_values":{"default":["IGK","IGL","IGG-L","VK","VL","K","L","LIGHT"],"items":{"maxLength":100,"minLength":1,"type":"string"},"maxItems":20,"minItems":1,"title":"Light-chain labels","type":"array","uniqueItems":true},"plate_column":{"default":null,"description":"When omitted, every row belongs to plate_1.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional plate column","type":["string","null"]},"plate_format":{"default":96,"enum":[96,384],"title":"Plate format","type":"integer"},"reading_frame":{"default":1,"enum":[1,2,3],"title":"One-based nucleotide reading frame","type":"integer"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"},"sequence_type":{"default":"nucleotide","enum":["nucleotide","protein"],"title":"Input sequence type","type":"string"},"well_column":{"default":"well","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Well column","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"analysis.pair_chains_by_identifier","description":"Pair antibody VH/VL, TCR alpha/beta, or custom left/right chains by an explicit identifier while retaining every ambiguous Cartesian combination and every unpaired record.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"records"}],"capability_id":"analysis.pair_chains_by_identifier","parameters":{"chain_column":"antpack_chain_type","left_chain_values":["H","VH","HEAVY"],"left_role_name":"heavy","pair_key_case_sensitive":true,"pairing_key_column":"pair_id","pairing_mode":"antibody","right_chain_values":["K","L","VK","VL","KAPPA","LAMBDA","LIGHT"],"right_role_name":"light","sequence_column":"sequence","sequence_type":"protein"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","nucleotide_sequences","annotated_sequences"],"description":"A frozen Selection or immutable sequence Dataset Version with explicit pairing key, chain label, and sequence columns.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"records","title":"Chain records"}],"limits":{"max_combinations_per_key":1000,"max_output_rows":100000,"max_rows_per_job":1,"max_sequence_characters":20000000,"max_sequence_length":100000,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Pair chains by identifier","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Every exact left-by-right chain combination plus explicit unpaired records, stable source identity, ambiguity evidence, and reproducibility digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"paired_chains","title":"Paired chain combinations"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native identifier-pairing response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native chain-pairing evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_column":{"default":"antpack_chain_type","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Chain label column","type":"string"},"left_chain_values":{"default":["H","VH","HEAVY"],"items":{"maxLength":100,"minLength":1,"type":"string"},"maxItems":20,"minItems":1,"title":"Left-role chain labels","type":"array","uniqueItems":true},"left_role_name":{"default":"heavy","maxLength":100,"minLength":1,"title":"Left role name","type":"string"},"pair_key_case_sensitive":{"default":true,"title":"Case-sensitive pairing keys","type":"boolean"},"pairing_key_column":{"default":"pair_id","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Pairing identifier column","type":"string"},"pairing_mode":{"default":"antibody","enum":["antibody","tcr","custom"],"title":"Pairing mode","type":"string"},"right_chain_values":{"default":["K","L","VK","VL","KAPPA","LAMBDA","LIGHT"],"items":{"maxLength":100,"minLength":1,"type":"string"},"maxItems":20,"minItems":1,"title":"Right-role chain labels","type":"array","uniqueItems":true},"right_role_name":{"default":"light","maxLength":100,"minLength":1,"title":"Right role name","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"},"sequence_type":{"default":"protein","enum":["protein","nucleotide"],"title":"Sequence type","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":2000,"max_rows_per_native_batch":2000,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_collective","successful_items_preserved":false},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"analysis.rank_alignment_diversity","description":"Rank every row in an immutable protein alignment with exact full-length gap-aware Hamming distance, deterministic farthest-first selection, and explicit cutoff evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"protein_aligned_sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"analysis.rank_alignment_diversity","parameters":{"aligned_sequence_column":"protein_aligned_sequence","cutoff_count":20,"minimum_marginal_distance":0.0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["alignment"],"description":"A frozen Selection or immutable ALIGNMENT Dataset Version containing equal-length gapped protein sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["protein_aligned_sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Aligned protein sequences"}],"limits":{"max_alignment_length":5000,"max_pairwise_character_comparisons":250000000,"max_rows_per_job":2000,"max_rows_per_native_batch":2000,"min_rows_per_job":2,"supported_alphabet":"aligned_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Rank alignment diversity","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Every source row in deterministic diversity order with exact mean and marginal gap-aware Hamming distances, cutoff status, and reproducibility evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"diversity_ranked_alignment","title":"Diversity-ranked alignment"},{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Frozen exact prefix selected by cutoff count and minimum marginal distance against the ranked output Version. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"diversity_selection","title":"Diversity cutoff Selection"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native ranking response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native diversity evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"aligned_sequence_column":{"default":"protein_aligned_sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Aligned protein column","type":"string"},"cutoff_count":{"default":20,"maximum":2000,"minimum":1,"title":"Maximum selected rows","type":"integer"},"minimum_marginal_distance":{"default":0.0,"description":"Stop the selected prefix when the next row's nearest-selected gap-aware Hamming distance is below this value.","maximum":1.0,"minimum":0.0,"title":"Minimum marginal distance","type":"number"},"seed_record_id":{"default":null,"maxLength":255,"minLength":1,"title":"Optional seed record ID","type":["string","null"]}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.2.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.back_translate_frequencies","description":"Select the exact maximum-weight amino acid at every submitted position and deterministically back-translate the resulting protein with a frozen standard DNA codon table, preserving complete frequency, tie, codon, and digest evidence without making a codon-optimization claim.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"records"}],"capability_id":"design.back_translate_frequencies","parameters":{"base_sequence_column":"cluster_representative_sequence","cluster_size_column":"cluster_size","codon_table_id":"standard_genetic_code_dna_v1","codon_tie_policy":"lexicographic_ascending","frequency_column":"cluster_variable_position_frequencies","frequency_mode":"cluster_variable_positions","label_column":"cluster_id","residue_tie_policy":"alphabetical_ascending"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["clusters","comparison","protein_sequences","annotated_sequences","table"],"description":"A frozen Selection or immutable Dataset Version containing complete position frequencies, or released cluster-variable frequencies together with an exact representative sequence and cluster size.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"records","title":"Amino-acid position frequencies"}],"limits":{"max_rows_per_job":1,"max_total_positions":5000,"min_rows_per_job":1,"supported_alphabet":"canonical_protein_frequencies"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Back-translate amino-acid frequencies","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing the exact frequency consensus protein, deterministic DNA back-translation, full position evidence, tie evidence, source-frequency inference evidence, codon-table digest, warnings, and result digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"generated_sequences","title":"Frequency-derived DNA sequences"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native request result with the frozen codon-table contract, exact submitted weights, selected residues and codons, warnings, row digests, and result digest.","media_type":"application/json","resource_kind":"artifact","role":"native_tool_output","title":"Native frequency back-translation evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"base_sequence_column":{"default":"cluster_representative_sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Representative sequence column","type":"string"},"cluster_size_column":{"default":"cluster_size","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Cluster size column","type":"string"},"codon_table_id":{"default":"standard_genetic_code_dna_v1","enum":["standard_genetic_code_dna_v1"],"title":"Frozen codon table","type":"string"},"codon_tie_policy":{"default":"lexicographic_ascending","enum":["lexicographic_ascending"],"title":"Synonymous-codon policy","type":"string"},"frequency_column":{"default":"cluster_variable_position_frequencies","description":"Ordered JSON array of one-based positions with residue_counts or residue_frequencies.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Frequency column","type":"string"},"frequency_mode":{"default":"cluster_variable_positions","description":"Complete positions require every position. Cluster-variable mode reconstructs omitted invariant positions from the exact representative sequence and cluster size.","enum":["complete_positions","cluster_variable_positions"],"title":"Frequency coverage","type":"string"},"label_column":{"default":"cluster_id","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Label column","type":["string","null"]},"residue_tie_policy":{"default":"alphabetical_ascending","enum":["alphabetical_ascending"],"title":"Residue tie policy","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.restriction_clone","description":"Digest exact insert DNA and one approved immutable vector Reference Library entry with a frozen enzyme registry, verify restriction sites and end compatibility, ligate forward or reverse constructs, and emit complete sequence, map, cut, provenance, lineage, and structured-skip evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"records"},{"resource_id":"<immutable-resource-id>","resource_kind":"reference","role":"vector"}],"capability_id":"design.restriction_clone","parameters":{"insert_left_enzyme":"EcoRI","insert_right_enzyme":"BamHI","label_column":"name","orientation":"forward","sequence_column":"sequence","vector_entry_id":"<vector_entry_id>","vector_left_enzyme":"EcoRI","vector_right_enzyme":"BamHI","vector_topology":"circular"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","annotated_sequences","alignment","table"],"description":"A frozen Selection or immutable Dataset Version containing exact unambiguous DNA inserts with their configured terminal recognition sites.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"records","title":"Restriction-flanked insert sequences"},{"dataset_kinds":[],"description":"One exact approved nucleotide Reference Library Version containing the selected checksum-bound vector entry and declared topology.","granularity":["reference_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["reference"],"role":"vector","title":"Approved vector Reference Library Version"}],"limits":{"max_references_per_job":1,"max_rows_per_job":1,"max_sequence_length":100000,"max_total_bases":1000000,"min_rows_per_job":1,"supported_alphabet":"unambiguous_dna"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Build restriction-cloned constructs","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing exact construct DNA or structured skips, vector provenance, checksums, topology, orientation, recognition/cut/overhang evidence, complete construct maps, warnings, and result digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"validated_constructs","title":"Restriction-cloned constructs"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native result with vector provenance, frozen enzyme registry, digestion and ligation evidence, skipped-row reasons, map evidence, row digests, and result digest.","media_type":"application/json","resource_kind":"artifact","role":"native_tool_output","title":"Native restriction-cloning evidence"},{"content_schema":null,"dataset_kind":null,"description":"Complete exact DNA sequences for every successfully validated construct with vector, topology, and checksum evidence in FASTA headers.","media_type":"text/x-fasta","resource_kind":"artifact","role":"construct_sequences","title":"Validated construct FASTA"},{"content_schema":null,"dataset_kind":null,"description":"Machine-readable construct segments, junctions, restriction sites, cut offsets, topology, checksums, vector provenance, skips, warnings, and result digest.","media_type":"application/json","resource_kind":"artifact","role":"construct_maps","title":"Validated construct maps"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"insert_left_enzyme":{"default":"EcoRI","enum":["BamHI","EcoRI","EcoRV","HindIII","NheI","NotI","SmaI","SpeI","XbaI","XhoI"],"title":"Insert left enzyme","type":"string"},"insert_right_enzyme":{"default":"BamHI","enum":["BamHI","EcoRI","EcoRV","HindIII","NheI","NotI","SmaI","SpeI","XbaI","XhoI"],"title":"Insert right enzyme","type":"string"},"label_column":{"default":"name","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Label column","type":["string","null"]},"orientation":{"default":"forward","enum":["forward","reverse"],"title":"Insert orientation","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Insert sequence column","type":"string"},"vector_entry_id":{"description":"Stable ID of the exact vector entry in the selected immutable Reference Library Version.","maxLength":200,"minLength":1,"title":"Vector entry","type":"string"},"vector_left_enzyme":{"default":"EcoRI","enum":["BamHI","EcoRI","EcoRV","HindIII","NheI","NotI","SmaI","SpeI","XbaI","XhoI"],"title":"Vector left enzyme","type":"string"},"vector_right_enzyme":{"default":"BamHI","enum":["BamHI","EcoRI","EcoRV","HindIII","NheI","NotI","SmaI","SpeI","XbaI","XhoI"],"title":"Vector right enzyme","type":"string"},"vector_topology":{"default":"circular","enum":["circular","linear"],"title":"Vector topology","type":"string"}},"required":["vector_entry_id","vector_topology","vector_left_enzyme","vector_right_enzyme","insert_left_enzyme","insert_right_enzyme"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"analytics","version":null},{"display_name":"antifold","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":2,"max_rows_per_native_batch":2,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"antifold.sample_antibody_sequences","description":"Sample deterministic, seed-bound antibody sequences from checksum-bound PDB structures with exact regional/global AntiFold scores, sequence recovery, mutation counts, and pinned-model evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"antifold.sample_antibody_sequences","parameters":{"exclude_heavy":false,"exclude_light":false,"heavy_chain":"H","light_chain":"L","num_sequences":10,"regions":["CDR1","CDR2","CDR3"],"sampling_temperature":0.2,"seed":42},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Dataset Version containing checksum-bound PDB Artifacts and their immutable structure evidence.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Antibody structures"}],"limits":{"max_antigen_residues":2000,"max_native_batch_size":2,"max_output_sequences_per_job":40,"max_pdb_bytes_per_job":4194304,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":2,"max_samples_per_record":20,"max_variable_domain_length":180,"min_rows_per_job":1,"min_variable_domain_length":40},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Sample antibody sequences with AntiFold","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable one-row-per-sample Dataset containing exact heavy/light sequences, regional and global AntiFold scores, sequence recovery, mutation count, sampling parameters, source structure identity, pinned-model evidence, and digests. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"sampled_sequences","title":"AntiFold-sampled antibody sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified AntiFold sampling response containing exact PDB, chain, seed, sampling, model, request, row, and batch evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AntiFold sampling result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"antigen_chain":{"default":null,"description":"Optional antigen PDB chain included as structural context and never sampled.","pattern":"^[A-Za-z0-9]$","title":"Antigen chain","type":["string","null"]},"exclude_heavy":{"default":false,"title":"Keep heavy chain fixed","type":"boolean"},"exclude_light":{"default":false,"title":"Keep light chain fixed","type":"boolean"},"heavy_chain":{"default":"H","description":"PDB chain containing the antibody heavy variable domain.","pattern":"^[A-Za-z0-9]$","title":"Heavy chain","type":["string","null"]},"light_chain":{"default":"L","description":"PDB chain containing the paired light variable domain. Paired sampling requires this chain.","pattern":"^[A-Za-z0-9]$","title":"Light chain","type":["string","null"]},"nanobody_chain":{"default":null,"description":"Single-chain nanobody PDB identifier. When supplied, heavy_chain and light_chain are ignored.","pattern":"^[A-Za-z0-9]$","title":"Nanobody chain","type":["string","null"]},"num_sequences":{"default":10,"maximum":20,"minimum":1,"title":"Sequences per structure","type":"integer"},"regions":{"default":["CDR1","CDR2","CDR3"],"description":"Official AntiFold IMGT region selectors. CDR1/CDR2/CDR3 apply to both antibody chains.","items":{"enum":["all","allH","allL","FWH","FWL","CDRH","CDRL","FW1","FW2","FW3","FW4","FWH1","FWH2","FWH3","FWH4","FWL1","FWL2","FWL3","FWL4","CDR1","CDR2","CDR3","CDRH1","CDRH2","CDRH3","CDRL1","CDRL2","CDRL3"],"type":"string"},"maxItems":12,"minItems":1,"title":"Regions to sample","type":"array","uniqueItems":true},"sampling_temperature":{"default":0.2,"maximum":1.0,"minimum":0.01,"title":"Sampling temperature","type":"number"},"seed":{"default":42,"maximum":2147483647,"minimum":0,"title":"Random seed","type":"integer"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":4,"max_rows_per_native_batch":4,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"antifold.score_antibody_structures","description":"Calculate exact per-residue AntiFold amino-acid log probabilities, top predictions, and perplexity for checksum-bound antibody PDB structures using the official pinned AntiFold model.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"antifold.score_antibody_structures","parameters":{"heavy_chain":"H","light_chain":"L"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Dataset Version containing checksum-bound PDB Artifacts and their immutable structure evidence.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Antibody structures"}],"limits":{"max_antigen_residues":2000,"max_native_batch_size":4,"max_pdb_bytes_per_job":8388608,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":4,"max_variable_domain_length":180,"min_rows_per_job":1,"min_variable_domain_length":40},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score antibody structures with AntiFold","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Structures Dataset containing exact per-residue AntiFold log probabilities, top predictions, perplexity summaries, structured row status, pinned-model evidence, and independently reconstructed digests. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"scored_structures","title":"AntiFold-scored antibody structures"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified AntiFold scoring response containing exact PDB, chain, residue, model, request, row, and batch evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AntiFold scoring result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"antigen_chain":{"default":null,"description":"Optional antigen PDB chain included as structural context but excluded from antibody residue scores.","pattern":"^[A-Za-z0-9]$","title":"Antigen chain","type":["string","null"]},"heavy_chain":{"default":"H","description":"PDB chain containing the antibody heavy variable domain. Set null only when nanobody_chain is supplied.","pattern":"^[A-Za-z0-9]$","title":"Heavy chain","type":["string","null"]},"light_chain":{"default":"L","description":"Optional PDB chain containing the paired light variable domain.","pattern":"^[A-Za-z0-9]$","title":"Light chain","type":["string","null"]},"nanobody_chain":{"default":null,"description":"Single-chain nanobody PDB identifier. When supplied, heavy_chain and light_chain are ignored.","pattern":"^[A-Za-z0-9]$","title":"Nanobody chain","type":["string","null"]}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":null,"tool_id":"antifold","version":null},{"display_name":"AntPack","license":"GPL-3.0-only","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"antpack.annotate_antibody_sequences","description":"Annotate antibody variable-region sequences with AntPack numbering, IMGT-derived FR/CDR regions, V/J germline assignments, explicitly labeled humanness evidence, and developability liabilities.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"antpack.annotate_antibody_sequences","parameters":{"include_liabilities":true,"mask_cdr3":false,"scheme":"imgt","sequence_column":"sequence","species":"human"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing antibody protein sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Antibody sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":500,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Annotate antibody sequences","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A complete typed result Artifact retaining source rows and normalized numbering, CDR, germline, humanness, and liability evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"annotated_sequences","title":"AntPack annotations"},{"content_schema":null,"dataset_kind":null,"description":"The immutable versioned AntPack batch response used for conformance and reproducibility.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native AntPack result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"cdr_scheme":{"default":null,"description":"Optional CDR definition used for liability context; null follows the numbering scheme.","enum":["imgt","chothia","kabat","aho",null],"title":"CDR definition","type":["string","null"]},"include_liabilities":{"default":true,"description":"Include AntPack CDR-context liability evidence with one-based source positions.","title":"Detect liabilities","type":"boolean"},"mask_cdr3":{"default":false,"description":"Exclude IMGT CDR3 from AntPack's human generative-model log-probability.","title":"Mask CDR3 in model score","type":"boolean"},"scheme":{"default":"imgt","description":"AntPack numbering scheme used for residue positions and V/J assignment.","enum":["imgt","chothia","kabat","aho"],"title":"Numbering scheme","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing amino-acid sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"},"species":{"default":"human","description":"Species database used for V/J assignment; unknown searches every supported AntPack database.","enum":["human","mouse","rabbit","alpaca","unknown"],"title":"Germline species","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"antpack.translate_antibody_dna","description":"Translate antibody nucleotide sequences with explicit frame/orientation selection, AntPack numbering evidence, ambiguity rejection, and complete per-candidate audit data.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"antpack.translate_antibody_dna","parameters":{"ambiguity_policy":"reject","include_row_roles":[],"orientation":"auto","scheme":"imgt","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","annotated_sequences","chromatograms","alignment"],"description":"A frozen Selection or immutable Dataset Version containing antibody DNA sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Antibody nucleotide sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":1800,"supported_alphabet":"nucleotide"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Translate antibody DNA","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A complete typed result Artifact retaining source DNA, the selected protein, exact frame/orientation, AntPack numbering evidence, and structured row failures. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"translated_sequences","title":"Translated antibody sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable AntPack response containing every evaluated frame and the versioned selection evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native translation evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"ambiguity_policy":{"default":"reject","description":"Reject scientifically tied candidates or apply an explicit deterministic preference after the evidence tie.","enum":["reject","prefer_forward_then_lowest_frame"],"title":"Scientific tie policy","type":"string"},"include_row_roles":{"default":[],"description":"Exact row-role values to translate; an empty list translates every bound row.","items":{"maxLength":100,"minLength":1,"type":"string"},"maxItems":20,"title":"Included row roles","type":"array","uniqueItems":true},"orientation":{"default":"auto","description":"Evaluate the forward strand, reverse complement, or both.","enum":["auto","forward","reverse_complement"],"title":"Orientation","type":"string"},"reading_frame":{"default":null,"description":"Optional zero-based frame from the evaluated orientation; null evaluates all three frames.","enum":[0,1,2,null],"title":"Reading frame","type":["integer","null"]},"row_role_column":{"default":null,"description":"Optional column used with include_row_roles to select consensus or other declared row roles before translation.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Row role column","type":["string","null"]},"scheme":{"default":"imgt","description":"Numbering scheme used to score antibody-frame candidates.","enum":["imgt","chothia","kabat","aho"],"title":"AntPack numbering scheme","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing nucleotide sequences; use accepted_sequence for reviewed chromatograms.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"DNA sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"antpack.validate_antibody_sequences","description":"Classify every immutable annotated antibody row as CORRECT, WARNING, or INCORRECT under an explicit scaffold policy and publish the exact CORRECT subset without dropping validation evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"antpack_chain_type":"<value>","antpack_numbering":"<value>","antpack_numbering_identity":"<value>","antpack_status":"<value>","sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"antpack.validate_antibody_sequences","parameters":{"ambiguous_codon_count_column":"translation_ambiguous_codon_count","ambiguous_sequence_severity":"warning","annotation_error_code_column":"antpack_error_code","annotation_status_column":"antpack_status","chain_type_column":"antpack_chain_type","high_liability_count_column":"antpack_liability_high_count","high_liability_severity":"warning","ignored_trailing_bases_column":"translation_ignored_trailing_bases","incomplete_terminal_codon_severity":"warning","incorrect_liability_score":-1000,"minimum_numbering_identity_fraction":0.6,"numbering_column":"antpack_numbering","numbering_identity_column":"antpack_numbering_identity","required_chain_type":"H","required_regions":["FR1","CDR1","FR2","CDR2","FR3","CDR3","FR4"],"secondary_peak_count_column":"source_secondary_peak_count","secondary_peak_severity":"warning","sequence_column":"sequence","stop_codon_count_column":"translation_stop_codon_count","warning_liability_score":-10},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["annotated_sequences"],"description":"A frozen Selection or immutable annotated Dataset Version containing sequence, AntPack status, chain, numbering identity, and numbered-region evidence.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence","antpack_status","antpack_chain_type","antpack_numbering_identity","antpack_numbering"],"resource_kinds":["inline"],"role":"sequences","title":"Annotated antibody sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":500,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Validate antibody sequences and extract CORRECT rows","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Every source row with exact CORRECT, WARNING, or INCORRECT classification, liability score, machine-readable reasons, and the complete policy snapshot. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"validated_sequences","title":"Validated antibody sequences"},{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A separate immutable Dataset containing exactly rows classified CORRECT under the persisted policy; WARNING and INCORRECT rows remain in the complete validated output. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"correct_sequences","title":"CORRECT antibody sequences"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified classification response and exact CORRECT identity list.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native antibody validation evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"ambiguous_codon_count_column":{"default":"translation_ambiguous_codon_count","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Translation ambiguous-codon count column","type":"string"},"ambiguous_sequence_severity":{"default":"warning","enum":["ignore","warning","incorrect"],"title":"Ambiguous sequence severity","type":"string"},"annotation_error_code_column":{"default":"antpack_error_code","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"AntPack error-code column","type":"string"},"annotation_status_column":{"default":"antpack_status","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"AntPack status column","type":"string"},"chain_type_column":{"default":"antpack_chain_type","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"AntPack chain-type column","type":"string"},"frameshift_column":{"default":null,"description":"Optional boolean evidence; frame offsets and trailing bases are never inferred to be frameshifts.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Explicit frameshift evidence column","type":["string","null"]},"high_liability_count_column":{"default":"antpack_liability_high_count","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"High-severity liability count column","type":"string"},"high_liability_severity":{"default":"warning","enum":["ignore","warning","incorrect"],"title":"High liability severity","type":"string"},"ignored_trailing_bases_column":{"default":"translation_ignored_trailing_bases","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Ignored trailing-base count column","type":"string"},"incomplete_terminal_codon_severity":{"default":"warning","enum":["ignore","warning","incorrect"],"title":"Incomplete terminal codon severity","type":"string"},"incorrect_liability_score":{"default":-1000,"maximum":-1,"title":"INCORRECT liability score","type":"integer"},"minimum_numbering_identity_fraction":{"default":0.6,"maximum":1.0,"minimum":0.0,"title":"Minimum numbering identity","type":["number","null"]},"numbering_column":{"default":"antpack_numbering","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Numbered-residue evidence column","type":"string"},"numbering_identity_column":{"default":"antpack_numbering_identity","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Numbering identity column","type":"string"},"required_chain_type":{"default":"H","enum":["H","K","L"],"title":"Required antibody chain","type":"string"},"required_regions":{"default":["FR1","CDR1","FR2","CDR2","FR3","CDR3","FR4"],"items":{"enum":["FR1","CDR1","FR2","CDR2","FR3","CDR3","FR4"],"type":"string"},"maxItems":7,"minItems":1,"title":"Required numbered regions","type":"array","uniqueItems":true},"secondary_peak_count_column":{"default":"source_secondary_peak_count","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Reviewed secondary-peak count column","type":"string"},"secondary_peak_severity":{"default":"warning","enum":["ignore","warning","incorrect"],"title":"Secondary peak severity","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Protein sequence column","type":"string"},"stop_codon_count_column":{"default":"translation_stop_codon_count","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Translation stop-codon count column","type":"string"},"warning_liability_score":{"default":-10,"maximum":0,"title":"WARNING liability score","type":"integer"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/jlparkI/AntPack","tool_id":"antpack","version":"0.3.8.5"},{"display_name":"ApexFold","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":16,"max_rows_per_native_batch":16,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"apexfold.predict_structural_plasticity","description":"Predict CD-like alpha-helical, beta-like, and unstructured peptide ensemble fractions across water, methanol/water, TFE/water, and SDS micelles for short canonical peptide sequences.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"peptide_sequences"}],"capability_id":"apexfold.predict_structural_plasticity","parameters":{"model_variant":"apexfold-esm-3seed","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing canonical 8-50-residue peptide sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"peptide_sequences","title":"Peptide sequences"}],"limits":{"max_native_batch_size":16,"max_rows_per_job":16,"max_sequence_length":50,"max_total_residues":800,"min_rows_per_job":1,"min_sequence_length":8,"supported_alphabet":"20_canonical_amino_acids"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict peptide structural plasticity with ApexFold","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset with four environment-specific secondary-structure fraction vectors, structural plasticity, and water-to-environment alpha-helix shifts. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"structural_plasticity_predictions","title":"ApexFold structural-plasticity predictions"},{"content_schema":null,"dataset_kind":null,"description":"The immutable native response and reproducibility evidence for the submitted peptide sequences.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native ApexFold result evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"model_variant":{"const":"apexfold-esm-3seed","default":"apexfold-esm-3seed","description":"The released three-seed ESM-2 150M ensemble; the AF3-cache variant is not general arbitrary-sequence inference.","title":"ApexFold model","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing one canonical peptide sequence per row.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://gitlab.com/machine-biology-group-public/apexfold","tool_id":"apexfold","version":"pinned 2026 release"},{"display_name":"BioPhi","license":"MIT; OASis reference data CC-BY-4.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":16,"max_rows_per_native_batch":16,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"biophi.humanize_antibody_sequences","description":"Humanize antibody variable domains with checksum-bound BioPhi Sapiens or human-germline CDR grafting and emit exact source/humanized residue-score matrices, numbered mutations, germline assignments, identities, and content digests.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"biophi.humanize_antibody_sequences","parameters":{"backmutate_vernier":false,"cdr_definition":"kabat","chain_type_column":"chain_type","humanize_cdrs":false,"iterations":1,"method":"sapiens","sapiens_refinement_iterations":0,"scheme":"kabat","sequence_column":"sequence","v_germline":"auto"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing antibody variable-domain amino-acid sequences and explicit H/K/L chain types, either per row or as one fixed parameter.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Antibody variable-domain sequences"}],"limits":{"max_native_batch_size":16,"max_rows_per_job":16,"max_sapiens_iterations":5,"max_total_residues":2880,"max_variable_domain_length":180,"min_rows_per_job":1,"min_variable_domain_length":40,"supported_alphabet":"unambiguous_protein","supported_chain_types":["H","K","L"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Humanize antibody sequences with BioPhi","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Annotated Sequences Dataset containing the humanized sequence, exact numbered mutations, source/humanized V/J assignments, sequence identity, complete source/humanized Sapiens residue-score matrices, structured row status, pinned-model evidence, and independently reconstructed digests. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"humanized_sequences","title":"BioPhi-humanized antibody sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified BioPhi response containing exact sequence, numbering, mutation, germline, Sapiens model, residue-score, request, row, and batch evidence. It contains no OASis score or substitute.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native BioPhi humanization result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"allOf":[{"if":{"properties":{"method":{"const":"sapiens"}}},"then":{"properties":{"sapiens_refinement_iterations":{"const":0},"v_germline":{"const":"auto"}}}},{"if":{"properties":{"method":{"const":"cdr_grafting"}}},"then":{"properties":{"humanize_cdrs":{"const":false},"iterations":{"const":1}}}},{"if":{"properties":{"humanize_cdrs":{"const":true}}},"then":{"properties":{"backmutate_vernier":{"const":false}}}}],"properties":{"backmutate_vernier":{"default":false,"description":"Restore parental Vernier residues after framework humanization or grafting.","title":"Backmutate Vernier residues","type":"boolean"},"cdr_definition":{"default":"kabat","enum":["kabat","imgt","chothia"],"title":"CDR definition","type":"string"},"chain_type":{"default":null,"description":"Optional H, K, or L value applied to every row. When supplied, it overrides chain_type_column.","enum":["H","K","L",null],"title":"Fixed chain type","type":["string","null"]},"chain_type_column":{"default":"chain_type","description":"Dataset column containing H, K, or L. It is required when fixed chain_type is null.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Chain-type column","type":["string","null"]},"humanize_cdrs":{"default":false,"description":"Allow Sapiens to mutate CDR residues. Cannot be combined with Vernier backmutation and does not apply to CDR grafting.","title":"Humanize CDRs","type":"boolean"},"iterations":{"default":1,"description":"Number of Sapiens humanization passes. CDR grafting requires the default value 1 and uses sapiens_refinement_iterations instead.","maximum":5,"minimum":1,"title":"Sapiens iterations","type":"integer"},"method":{"default":"sapiens","enum":["sapiens","cdr_grafting"],"title":"Humanization method","type":"string"},"sapiens_refinement_iterations":{"default":0,"description":"Optional Sapiens refinement passes after CDR grafting. Sapiens humanization requires zero here.","maximum":5,"minimum":0,"title":"Post-graft Sapiens iterations","type":"integer"},"scheme":{"default":"kabat","enum":["kabat","imgt","chothia"],"title":"Numbering scheme","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing the antibody variable-domain amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"},"v_germline":{"default":"auto","description":"Use auto or an explicit human V-germline name for CDR grafting. Sapiens requires auto.","maxLength":64,"minLength":1,"title":"CDR-grafting V germline","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":16,"max_rows_per_native_batch":16,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"biophi.score_oasis_humanness","description":"Measure exact overlapping 9-mer prevalence against the checksum-qualified official OASis database, returning OASis identity, therapeutic-mAb percentile, per-peptide subject prevalence, and numbered residue overlap evidence without substituting germline or Sapiens scores.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"biophi.score_oasis_humanness","parameters":{"cdr_definition":"kabat","chain_type_column":"chain_type","min_fraction_subjects":0.1,"scheme":"kabat","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing antibody variable-domain amino-acid sequences and explicit heavy, kappa, or lambda chain types, either per row or as one fixed parameter.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Antibody variable-domain sequences"}],"limits":{"max_complete_peptide_rows":2752,"max_native_batch_size":16,"max_rows_per_job":16,"max_total_residues":2880,"max_variable_domain_length":180,"min_rows_per_job":1,"min_variable_domain_length":40,"peptide_length":9,"supported_alphabet":"unambiguous_protein","supported_chain_types":["H","K","L"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score antibody repertoire humanness with BioPhi OASis","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Annotated Sequences Dataset containing exact OASis identity and therapeutic-mAb percentile fractions, human/non-human overlapping 9-mer counts, per-peptide OAS subject prevalence, residue-linked overlap burden, numbering/region evidence, structured row status, official-database evidence, and independently reconstructed digests. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"oasis_scores","title":"BioPhi OASis humanness scores"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified OASis response containing the complete exact 9-mer and numbered-residue evidence, selected subject-prevalence threshold, official database/license/checksum pins, request/row/result digests, and explicit repertoire-proxy semantics.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native BioPhi OASis result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"cdr_definition":{"default":"kabat","enum":["kabat","imgt","chothia","north"],"title":"CDR definition","type":"string"},"chain_type":{"default":null,"description":"Optional H, K, or L value applied to every row. When supplied, it overrides chain_type_column.","enum":["H","K","L",null],"title":"Fixed chain type","type":["string","null"]},"chain_type_column":{"default":"chain_type","description":"Dataset column containing H/heavy, K/kappa, or L/lambda. It is required when fixed chain_type is null.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Chain-type column","type":["string","null"]},"min_fraction_subjects":{"default":0.1,"description":"A 9-mer is human-like when it occurs in at least this fraction of eligible OAS subjects. Values use whole percentage-point increments; 0.01, 0.10, 0.50, and 0.90 are the established loose, relaxed, medium, and strict presets.","maximum":0.9,"minimum":0.01,"multipleOf":0.01,"title":"Minimum OAS subject prevalence","type":"number"},"scheme":{"default":"kabat","enum":["kabat","imgt","chothia","aho"],"title":"Numbering scheme","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing the antibody variable-domain amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/Merck/BioPhi","tool_id":"biophi","version":"1.0.11"},{"display_name":"BoltzGen","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"boltzgen.design_binders","description":"Generate a bounded, target- and epitope-conditioned protein or peptide binder cohort with the pinned BoltzGen runtime, checksum-bound target structures, deterministic fixed-seed replay, and explicit native filter outcomes.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"binding_residues":"<value>","structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","target_chain":"<value>","target_sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"targets"}],"capability_id":"boltzgen.design_binders","parameters":{"binder_max_length":120,"binder_min_length":40,"binding_residues_column":"binding_residues","model_profile":"adherence","num_designs":4,"protocol":"protein-anything","seed":0,"target_chain_column":"target_chain"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One immutable target structure with its target chain and an explicit non-empty epitope residue set. The product adapter downloads and verifies the exact Artifact before native dispatch.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256","target_sequence","target_chain","binding_residues"],"resource_kinds":["inline"],"role":"targets","title":"Target structures"}],"limits":{"max_binding_residues":32,"max_designs_per_row":4,"max_output_bytes_per_job":16777216,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":1,"max_rows_per_native_batch":1,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design binders with BoltzGen","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable candidate Dataset retaining target and epitope context, exact designed sequences, native metrics, filter decisions, and checksum-bound complex Artifacts—including scientifically valid zero-survivor campaigns. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"candidate_cohort","title":"Target-conditioned binder candidates"},{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified complex produced by the exact released BoltzGen image.","media_type":"chemical/x-mmcif","resource_kind":"artifact","role":"designed_complex","title":"Designed target-binder complex"},{"content_schema":null,"dataset_kind":null,"description":"The immutable native result containing request, model, runtime, metrics, structure, filter, and digest evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native BoltzGen result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"binder_max_length":{"default":120,"maximum":160,"minimum":8,"title":"Maximum binder length","type":"integer"},"binder_min_length":{"default":40,"maximum":160,"minimum":8,"title":"Minimum binder length","type":"integer"},"binding_residues_column":{"default":"binding_residues","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Binding-residue column","type":"string"},"model_profile":{"default":"adherence","enum":["adherence","diverse"],"title":"BoltzGen design checkpoint profile","type":"string"},"num_designs":{"default":4,"maximum":4,"minimum":1,"type":"integer"},"protocol":{"default":"protein-anything","enum":["protein-anything","peptide-anything"],"type":"string"},"seed":{"default":0,"maximum":2147483647,"minimum":0,"type":"integer"},"target_chain_column":{"default":"target_chain","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Target-chain column","type":"string"}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"boltzgen.design_small_molecule_binders","description":"Generate de novo protein binders around one CCD or SMILES small molecule with upstream BoltzGen protein-small_molecule diffusion and affinity output.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"ligand_identifier":"<value>","ligand_identifier_type":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"ligands"}],"capability_id":"boltzgen.design_small_molecule_binders","parameters":{"binder_max_length":140,"binder_min_length":100,"model_profile":"adherence","num_designs":4,"protocol":"protein-small_molecule","seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["table","assay"],"description":"One lipid or small molecule identified by CCD code or isomeric SMILES.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["ligand_identifier_type","ligand_identifier"],"resource_kinds":["inline"],"role":"ligands","title":"Ligand identity"}],"limits":{"max_designs_per_job":4,"max_rows_per_job":1,"max_sequence_length":180,"max_smiles_bytes":4096,"min_rows_per_job":1,"min_sequence_length":40},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design small-molecule binders with BoltzGen","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable Dataset of generated protein-small-molecule complexes with exact ligand identity, sequence, metrics, and checksum-bound structure Artifacts. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"generated_structures","title":"Small-molecule binder candidates"},{"content_schema":null,"dataset_kind":null,"description":"The immutable validated native result, request digest, runtime identity, and artifact inventory.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native BoltzGen small-molecule result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"binder_max_length":{"default":140,"description":"Maximum generated binder-chain length in residues.","maximum":180,"minimum":40,"title":"Maximum binder length","type":"integer"},"binder_min_length":{"default":100,"description":"Minimum generated binder-chain length in residues.","maximum":180,"minimum":40,"title":"Minimum binder length","type":"integer"},"model_profile":{"default":"adherence","description":"Use the adherence profile for target-focused designs or diverse for broader sampling.","enum":["adherence","diverse"],"title":"Model profile","type":"string"},"num_designs":{"default":4,"description":"Number of complex structures generated in this job.","maximum":4,"minimum":1,"title":"Designs","type":"integer"},"protocol":{"const":"protein-small_molecule","default":"protein-small_molecule","description":"Pinned BoltzGen protein–small-molecule binder protocol.","title":"Protocol","type":"string"},"seed":{"default":0,"description":"Non-negative deterministic sampling seed.","maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"}},"type":"object"},"resource_class":"gpu-medium","side_effect_class":"expensive_compute","version":"1.2.0"}],"source_repository":"https://github.com/HannesStark/boltzgen","tool_id":"boltzgen","version":"0.3.2-derived pinned release profile"},{"display_name":"Caliby","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"caliby.design_or_score_sequences","description":"Design or score structure-conditioned protein sequences with all five released Caliby and SolubleCaliby model profiles.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"caliby.design_or_score_sequences","parameters":{"batch_size":4,"model":"soluble_caliby","num_sequences":4,"omit_amino_acids":[],"operation":"design_single","seed":0,"temperature":0.01},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One checksum-bound protein structure for single modes, or two to 32 ordered, aligned conformers for ensemble modes.","granularity":["selection","dataset_version"],"max_items":32,"media_types":["chemical/x-pdb","chemical/x-mmcif"],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256","structure_media_type"],"resource_kinds":["inline"],"role":"structures","title":"Protein structure or aligned conformer ensemble"}],"limits":{"max_conformers":32,"max_rows_per_job":1,"max_sequences_per_job":64,"max_structure_bytes":2000000,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design or score protein sequences with Caliby","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable Dataset containing designed or scored sequences, global U values, optional per-residue scores, exact checkpoint identity, and links to designed structures. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"caliby_results","title":"Caliby designed sequences and scores"},{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified Caliby design threaded onto the supplied protein backbone.","media_type":"chemical/x-mmcif","resource_kind":"artifact","role":"designed_structure","title":"Caliby designed structure"},{"content_schema":null,"dataset_kind":null,"description":"The immutable validated native result with request, source, checkpoint, and score evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Caliby result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"amino_acid_restrictions":{"description":"Optional native Caliby amino-acid restriction expression.","maxLength":8000,"title":"Amino-acid restrictions","type":["string","null"]},"batch_size":{"default":4,"description":"Internal sequential inference batch size.","maximum":16,"minimum":1,"title":"Inference batch size","type":"integer"},"fixed_positions":{"description":"Optional native Caliby fixed-position expression.","maxLength":4000,"title":"Fixed positions","type":["string","null"]},"model":{"default":"soluble_caliby","description":"Released Caliby checkpoint profile.","enum":["caliby","soluble_caliby","soluble_caliby_v1","caliby_distill","soluble_caliby_distill"],"title":"Model","type":"string"},"num_sequences":{"default":4,"description":"Number of sequences to design. Scoring modes require the default value because they score the input sequence.","maximum":64,"minimum":1,"title":"Designed sequences","type":"integer"},"omit_amino_acids":{"default":[],"description":"Unique one-letter amino-acid codes excluded during design.","items":{"enum":["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"],"type":"string"},"maxItems":20,"title":"Omit amino acids","type":"array","uniqueItems":true},"operation":{"default":"design_single","description":"Design sequences or score the sequence already present in one structure or an aligned conformer ensemble.","enum":["design_single","design_ensemble","score_single","score_ensemble"],"title":"Operation","type":"string"},"seed":{"default":0,"description":"Deterministic sampling seed used by design operations; scoring operations preserve it in request provenance.","maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"},"symmetry_positions":{"description":"Optional native Caliby symmetry-position expression.","maxLength":8000,"title":"Symmetry positions","type":["string","null"]},"temperature":{"default":0.01,"description":"Sampling temperature for design modes.","exclusiveMinimum":0.0,"maximum":2.0,"title":"Temperature","type":"number"}},"type":"object"},"resource_class":"gpu-medium","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://github.com/ProteinDesignLab/caliby","tool_id":"caliby","version":"0.1.0 pinned source profile"},{"display_name":"clustering","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"clustering.cluster_protein_sequences","description":"Cluster an ordered immutable protein batch, or an explicitly oriented and framed DNA translation, with digest-pinned CD-HIT, exact representative/member evidence, bounded sparse position frequencies, and no external data mutation.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"clustering.cluster_protein_sequences","parameters":{"identity":0.9,"include_statuses":[],"region_label":"full_sequence","sequence_column":"sequence","translation_ambiguity_policy":"reject","translation_frame":0,"translation_mode":"none","translation_orientation":"forward","translation_stop_policy":"reject"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing protein, nucleotide, or annotated antibody sequences. DNA inputs require explicit translation parameters.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":2000,"supported_alphabet":"protein_or_dna_with_explicit_translation"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Cluster protein sequences","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A complete typed result Artifact retaining source fields, cluster, representative, identity, size, evenness, sparse position-frequency evidence, and the exact protein or explicit DNA translation supplied to native CD-HIT. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"clustered_sequences","title":"Clustered protein sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable versioned CD-HIT response containing every cluster, member, metric, and digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native CD-HIT evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"identity":{"default":0.9,"description":"CD-HIT identity cutoff as a fraction.","maximum":1.0,"minimum":0.4,"title":"Minimum sequence identity","type":"number"},"include_statuses":{"default":[],"description":"Exact status values to cluster; an empty list clusters every bound row.","items":{"maxLength":100,"minLength":1,"type":"string"},"maxItems":20,"title":"Included statuses","type":"array","uniqueItems":true},"region_label":{"default":"full_sequence","description":"Honest label for the sequence region supplied to clustering.","maxLength":100,"minLength":1,"title":"Region label","type":"string"},"row_status_column":{"default":null,"description":"Optional status column used with include_statuses before clustering.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Row status column","type":["string","null"]},"sequence_column":{"default":"sequence","description":"Protein column clustered by CD-HIT, such as sequence or antpack_cdr3.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Clustering sequence column","type":"string"},"translation_ambiguity_policy":{"default":"reject","description":"Reject ambiguous codons or translate them to X with an exact row-level count.","enum":["reject","translate_x"],"title":"Ambiguous codon policy","type":"string"},"translation_frame":{"default":0,"description":"Explicit zero-based reading frame used when translation_mode is coding_dna.","maximum":2,"minimum":0,"title":"DNA reading frame","type":"integer"},"translation_mode":{"default":"none","description":"Use none for protein input or coding_dna to translate the selected nucleotide column before CD-HIT.","enum":["none","coding_dna"],"title":"Translation mode","type":"string"},"translation_orientation":{"default":"forward","description":"Explicit orientation used when translation_mode is coding_dna.","enum":["forward","reverse_complement"],"title":"DNA orientation","type":"string"},"translation_stop_policy":{"default":"reject","description":"Reject every translated stop, or remove one terminal stop while still rejecting internal stops.","enum":["reject","trim_terminal"],"title":"Stop codon policy","type":"string"},"word_length":{"default":null,"description":"Optional threshold-compatible CD-HIT word length; null selects 2/3/4/5 from identity.","maximum":5,"minimum":2,"title":"CD-HIT word length","type":["integer","null"]}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":null,"tool_id":"clustering","version":null},{"display_name":"DeepViscosity","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"deepviscosity.predict_batch","description":"Classify high-concentration antibody viscosity for paired heavy- and light-chain sequences with DeepViscosity and preserve the model ensemble evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"heavy_chain":"<value>","light_chain":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"deepviscosity.predict_batch","parameters":{"heavy_chain_column":"heavy_chain","light_chain_column":"light_chain"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version with paired heavy- and light-chain protein sequences in each row.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["heavy_chain","light_chain"],"resource_kinds":["inline"],"role":"sequences","title":"Paired antibody sequences"}],"limits":{"expected_feature_count":30,"max_rows_per_job":1,"max_sequence_length":500,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict antibody viscosity","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A complete typed result Artifact retaining each antibody pair with normalized viscosity class, probability, uncertainty, row status, and DeepSP features. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"viscosity_predictions","title":"Viscosity predictions"},{"content_schema":null,"dataset_kind":null,"description":"The immutable terminal native response including partial row failures and the model-bundle execution pin.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native DeepViscosity result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_chain_column":{"default":"heavy_chain","description":"Dataset column containing the heavy-chain amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy-chain column","type":"string"},"light_chain_column":{"default":"light_chain","description":"Dataset column containing the light-chain amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Light-chain column","type":"string"},"name_column":{"default":null,"description":"Optional Dataset column used as the antibody name in native output.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Name column","type":["string","null"]}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://github.com/Lailabcode/DeepViscosity","tool_id":"deepviscosity","version":"1.0.0"},{"display_name":"DELPHI","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":32,"max_rows_per_native_batch":32,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"delphi.predict_psr","description":"Estimate polyreactivity assay pass probability from paired VH/VL and explicit HCDR3 using the IPI one-hot Transformer.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"hcdr3":"<value>","heavy_sequence":"<value>","light_sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"antibodies"}],"capability_id":"delphi.predict_psr","parameters":{},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["annotated_sequences"],"description":"VH, VL, and caller-annotated HCDR3 (IMGT 105–117 without framework anchors).","granularity":["inline"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["heavy_sequence","light_sequence","hcdr3"],"resource_kinds":["inline"],"role":"antibodies","title":"Paired antibody sequences"}],"limits":{"max_hcdr3_length":25,"max_native_batch_size":32,"max_rows_per_job":32,"max_sequence_length":135,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict antibody polyreactivity with DELPHI","outputs":[{"content_schema":null,"dataset_kind":null,"description":"Per-antibody pass probabilities, classifications, exact sequences, and threshold/model provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Antibody assay predictions"}],"parameters_schema":{"additionalProperties":false,"properties":{},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":32,"max_rows_per_native_batch":32,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"delphi.predict_sec","description":"Estimate SEC monomer purity assay pass probability from paired VH/VL and explicit HCDR3 using the IPI one-hot Transformer.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"hcdr3":"<value>","heavy_sequence":"<value>","light_sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"antibodies"}],"capability_id":"delphi.predict_sec","parameters":{},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["annotated_sequences"],"description":"VH, VL, and caller-annotated HCDR3 (IMGT 105–117 without framework anchors).","granularity":["inline"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["heavy_sequence","light_sequence","hcdr3"],"resource_kinds":["inline"],"role":"antibodies","title":"Paired antibody sequences"}],"limits":{"max_hcdr3_length":25,"max_native_batch_size":32,"max_rows_per_job":32,"max_sequence_length":135,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict antibody SEC monomer purity with DELPHI","outputs":[{"content_schema":null,"dataset_kind":null,"description":"Per-antibody pass probabilities, classifications, exact sequences, and threshold/model provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Antibody assay predictions"}],"parameters_schema":{"additionalProperties":false,"properties":{},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/proteininnovation/delphi","tool_id":"delphi","version":"v4 model release"},{"display_name":"DISCO","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":8,"max_rows_per_native_batch":8,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"disco.design_ligand_conditioned_proteins","description":"Jointly co-design protein sequences and structures with DISCO in unconditional, exact-SDF ligand-conditioned, DNA-conditioned, or RNA-conditioned mode. One bounded request runs up to eight mixed rows and four shared seeds in one model-loading process.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"id":"<value>","mode":"<value>","protein_length":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"design_context"}],"capability_id":"disco.design_ligand_conditioned_proteins","parameters":{"effort":"fast","experiment":"designable","seeds":[0]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures","table"],"description":"One to eight immutable design rows containing a mode, protein length, and mode-specific exact SDF or DNA/RNA conditioner.","granularity":["selection","dataset_version"],"max_items":8,"media_types":["chemical/x-mdl-sdfile","application/json"],"min_items":1,"ordered":true,"required":true,"required_fields":["id","mode","protein_length"],"resource_kinds":["inline"],"role":"design_context","title":"DISCO design cohort"}],"limits":{"max_designs_per_job":32,"max_ligand_atoms":256,"max_ligand_bytes":1048576,"max_native_seconds":10800,"max_rows_per_job":8,"max_rows_per_native_batch":8,"max_seeds_per_row":4,"max_sequence_length":500,"min_rows_per_job":1,"min_sequence_length":30},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Co-design general protein complexes with DISCO","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable Structures Dataset of ordered DISCO batch outputs with conditioning mode, sequence, seed, structure, and checksum evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_structures","title":"DISCO designed structures"},{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified designed sequence and structure from an unconditional, ligand-, DNA-, or RNA-conditioned row.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"designed_structure","title":"DISCO designed protein"},{"content_schema":null,"dataset_kind":null,"description":"The immutable ordered native result with per-row seeds, files, model identity, and batch-execution evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native DISCO batch result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"effort":{"default":"fast","enum":["fast","max"],"type":"string"},"experiment":{"default":"designable","enum":["designable","diverse"],"type":"string"},"seeds":{"default":[0],"items":{"maximum":2147483643,"minimum":0,"type":"integer"},"maxItems":4,"minItems":1,"type":"array","uniqueItems":true}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"1.4.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"disco.design_protein_structures","description":"Generate one deterministic 40-residue protein sequence and matching structure from scratch with the pinned DISCO model on the H100-qualified compatibility route. Expanded length, batch, effort, experiment, ligand, DNA, and RNA capabilities are available through the general DISCO operation.","example":{"bindings":[],"capability_id":"disco.design_protein_structures","parameters":{"designs":1,"effort":"fast","experiment":"designable","length":40,"mode":"unconditional","seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_pdb_bytes_per_row":2097152,"max_rows_per_job":1,"max_samples_per_row":1,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Co-design a protein sequence and structure with DISCO","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The 40-residue structure generated jointly with its protein sequence.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"predicted_structure","title":"Designed protein structure"},{"content_schema":null,"dataset_kind":null,"description":"The protein sequence co-designed with the published structure.","media_type":"text/plain","resource_kind":"artifact","role":"designed_sequence","title":"Designed protein sequence"},{"content_schema":null,"dataset_kind":null,"description":"Machine-readable output retained for result validation.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native DISCO result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"designs":{"const":1,"default":1},"effort":{"const":"fast","default":"fast"},"experiment":{"const":"designable","default":"designable"},"length":{"const":40,"default":40},"mode":{"const":"unconditional","default":"unconditional"},"seed":{"const":0,"default":0}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://github.com/DISCO-Design/DISCO","tool_id":"disco","version":"pinned 2026 release profile"},{"display_name":"DockQ","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":25,"max_rows_per_native_batch":25,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"dockq.score_complexes","description":"Calculate DockQ 2.1.3 scores for a bounded cohort of checksum-bound predicted and reference complexes with explicit chain mapping, alignment policy, complete interface evidence, and structured row failure.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"model_structure_artifact_id":"<value>","model_structure_checksum_sha256":"<value>","model_structure_media_type":"<value>","reference_structure_artifact_id":"<value>","reference_structure_checksum_sha256":"<value>","reference_structure_media_type":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"complex_pairs"}],"capability_id":"dockq.score_complexes","parameters":{"allowed_mismatches":0,"no_align":false},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures","comparison"],"description":"One frozen Selection or immutable Dataset Version containing checksum-bound predicted and reference complex Artifacts for every row.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["model_structure_artifact_id","model_structure_media_type","model_structure_checksum_sha256","reference_structure_artifact_id","reference_structure_media_type","reference_structure_checksum_sha256"],"resource_kinds":["inline"],"role":"complex_pairs","title":"Predicted and reference complex pairs"}],"limits":{"max_output_bytes_per_role":50000000,"max_rows_per_job":25,"max_rows_per_native_batch":25,"max_structure_bytes_per_job":30000000,"max_structure_bytes_per_row":5000000,"min_rows_per_job":1,"supported_media_types":["chemical/x-pdb","chemical/x-mmcif"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score predicted complexes with DockQ","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset containing DockQ, interface, RMSD, chain-mapping, alignment, and explicit row-failure evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"dockq_scores","title":"DockQ reference-comparison scores"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified DockQ 2.1.3 cohort response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native DockQ result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"allowed_mismatches":{"default":0,"maximum":20,"minimum":0,"title":"Allowed sequence mismatches","type":"integer"},"mapping_column":{"default":null,"description":"Optional Dataset column containing explicit DockQ chain mappings such as AB:AB.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Chain-mapping column","type":["string","null"]},"no_align":{"default":false,"description":"Disable DockQ sequence alignment only when residue correspondence is already exact.","title":"Disable sequence alignment","type":"boolean"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"2.1.3"}],"source_repository":"https://github.com/bjornwallner/DockQ","tool_id":"dockq","version":"2.1.3"},{"display_name":"ESM CPU","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"esm.embed_protein_sequences","description":"Compute mean-pooled protein embeddings with the published sub-1B Biohub ESMC 300M or 600M checkpoints on CPU.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"esm.embed_protein_sequences","parameters":{"model":"esmc-300m","pooling":"mean","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing protein amino-acid sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":2046,"max_total_residues":4096,"supported_alphabet":"20_canonical_amino_acids_plus_X"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Embed protein sequences with ESM","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version containing the exact mean embedding, dimension, model, and checksum evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"sequence_embeddings","title":"ESM sequence embeddings"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-verified native response and exact CPU checkpoint identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"ESM native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"model":{"default":"esmc-300m","description":"Exact published sub-1B checkpoint admitted by the public CPU runtime.","enum":["esmc-300m","esmc-600m"],"title":"Model","type":"string"},"pooling":{"const":"mean","default":"mean","title":"Pooling","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://github.com/Biohub/esm","tool_id":"esm","version":"ESM 2026 published base family; ESM2-compatible ESMC 300M/600M public tier"},{"display_name":"ESM GPU","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"esm_gpu.embed_protein_sequences","description":"Compute mean-pooled protein embeddings with ESMC-6B or the open ESM3 small model on the approved H100 runtime.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"esm_gpu.embed_protein_sequences","parameters":{"model":"esm3-sm-open-v1","pooling":"mean","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing protein amino-acid sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":2046,"max_total_residues":4096,"supported_alphabet":"20_canonical_amino_acids_plus_X"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Embed protein sequences with large ESM models","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version containing the exact mean embedding, dimension, model revision, and checksum evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"sequence_embeddings","title":"Large ESM sequence embeddings"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-verified native response with the exact H100 runtime and checkpoint identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Large ESM native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"model":{"default":"esm3-sm-open-v1","description":"Exact published model admitted by the Pro/Enterprise H100 runtime.","enum":["esm3-sm-open-v1","esmc-6b"],"title":"Model","type":"string"},"pooling":{"const":"mean","default":"mean","title":"Pooling","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"0.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"esm_gpu.generate_protein_sequence","description":"Fill masked amino-acid positions with the open ESM3 small generative model using bounded, seeded decoding.","example":{"bindings":[],"capability_id":"esm_gpu.generate_protein_sequence","parameters":{"model":"esm3-sm-open-v1","num_steps":32,"prompt":"<prompt>","seed":0,"temperature":0.7,"top_p":0.95},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_generation_steps":128,"max_prompt_length":512,"required_mask_token":"_"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Generate masked protein sequence with ESM3","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A checksum-bound Dataset Version containing the seeded sequence completing the submitted masked prompt. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"generated_sequences","title":"ESM3 generated protein sequences"},{"content_schema":null,"dataset_kind":null,"description":"The validated prompt, sequence, seed, decoding settings, model revision, and H100 runtime evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"ESM3 generation evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"model":{"const":"esm3-sm-open-v1","default":"esm3-sm-open-v1","title":"Model","type":"string"},"num_steps":{"default":32,"maximum":128,"minimum":1,"title":"Generation steps","type":"integer"},"prompt":{"description":"Protein sequence containing at least one underscore mask position.","maxLength":512,"minLength":8,"pattern":"^[ACDEFGHIKLMNPQRSTVWYX_]+$","title":"Masked protein sequence","type":"string"},"seed":{"default":0,"maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"},"temperature":{"default":0.7,"maximum":1.5,"minimum":0,"title":"Temperature","type":"number"},"top_p":{"default":0.95,"exclusiveMinimum":0,"maximum":1,"title":"Top-p","type":"number"}},"required":["prompt"],"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"0.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"esm_gpu.predict_protein_structure","description":"Predict monomer or bounded multichain protein structures with ESMFold2 or ESMFold2-Fast, both conditioned on the published ESMC-6B base model.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"chains"}],"capability_id":"esm_gpu.predict_protein_structure","parameters":{"model":"esmfold2-fast","num_loops":10,"num_sampling_steps":50,"seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing one to four protein chains per requested structure.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"chains","title":"Protein chains"}],"limits":{"max_chains":4,"max_num_loops_times_sampling_steps":1000,"max_rows_per_job":1,"max_total_residues":512,"supported_alphabet":"20_canonical_amino_acids_plus_X"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict protein structure with ESMFold2","outputs":[{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified mmCIF Artifact from the selected seeded ESMFold2 model.","media_type":"chemical/x-mmcif","resource_kind":"artifact","role":"predicted_structure","title":"ESMFold2 predicted structure"},{"content_schema":null,"dataset_kind":null,"description":"The validated structure checksum, confidence values, request digest, model revisions, and H100 runtime identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"ESMFold2 confidence and runtime evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"model":{"default":"esmfold2-fast","enum":["esmfold2","esmfold2-fast"],"title":"Model","type":"string"},"num_loops":{"default":10,"enum":[5,10,20],"title":"Recycling loops","type":"integer"},"num_sampling_steps":{"default":50,"enum":[25,50,100],"title":"Diffusion sampling steps","type":"integer"},"seed":{"default":0,"maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://github.com/Biohub/esm","tool_id":"esm-gpu","version":"ESMC-6B, ESM3-open, and ESMFold2 published base family"},{"display_name":"Fc engineering","license":"MIT (Fc Variant Atlas); Biopython license (alignment runtime)","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":100,"max_rows_per_native_batch":100,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"fc_analysis.identify_and_compare","description":"Map full protein chains to sourced human-IgG EU references, inspect sequence-compatible Fc designs and generate explicit same-Fab candidate edits. Report partial coverage, hybrid candidates, disputes, extra differences and row failures without inferring glycosylation or activity.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"fc_analysis.identify_and_compare","parameters":{"sequence_column":"sequence","variant_ids":[]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"One unique protein chain per row. Retain chain identity and source construct labels for asymmetric molecules.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Full-chain or Fc protein sequences"}],"limits":{"max_input_characters":60000,"max_rows_per_job":100,"max_rows_per_native_batch":100,"max_sequence_length":1500,"supported_alphabet":"standard_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Identify Fc sequences and compare explicit constructs","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Every input chain retains residue mapping, reference differences, source-compatible designs, explicit failures and any requested candidate sequence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"fc_annotated_sequences","title":"Fc sequence and construct evidence"},{"content_schema":null,"dataset_kind":null,"description":"Exact source-attributed native cohort response with sequence and result digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Fc cohort evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"reference_isotype":{"default":null,"enum":[null,"IgG1","IgG2","IgG3","IgG4"],"title":"Reference isotype (optional)","type":["string","null"]},"reference_isotype_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional per-chain reference isotype column","type":["string","null"]},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Protein sequence column","type":"string"},"variant_ids":{"default":[],"items":{"maxLength":120,"type":"string"},"maxItems":8,"title":"Fc designs to apply (empty identifies only)","type":"array","uniqueItems":true},"variant_ids_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional per-chain design list column","type":["string","null"]}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/dataRichinsightPoor/fc-variant-atlas","tool_id":"fc-engineering","version":"Fc Variant Atlas 1.1.0; Ubi analysis 1.0.0"},{"display_name":"FoldCraft","license":"MIT source; ColabDesign Beer-Ware Revision 42; AlphaFold parameters CC-BY-4.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"foldcraft.design_protein_binders","description":"Design up to four protein-binder trajectories against one checksum-bound target in a single pinned FoldCraft/ColabDesign process, reusing the ProteinMPNN load and preserving ordered per-item output identity.","example":{"bindings":[{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"binder_template"},{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"target_template"}],"capability_id":"foldcraft.design_protein_binders","parameters":{"binder_chain":"A","binder_hotspots":"","binder_mask":"","design_stages":"100,100,20","mpnn_samples":1,"mpnn_weight":"soluble","num_designs":1,"redesign_method":"non-interface","target_chain":"A","target_hotspots":"<target_hotspots>"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One immutable binder-template PDB Artifact whose exact bytes and SHA-256 are bound to the Run.","granularity":["asset"],"max_items":1,"media_types":["chemical/x-pdb"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"binder_template","title":"Binder template"},{"dataset_kinds":["structures"],"description":"One immutable target-template PDB Artifact whose exact bytes and SHA-256 are bound to the Run.","granularity":["asset"],"max_items":1,"media_types":["chemical/x-pdb"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"target_template","title":"Target structure"}],"limits":{"max_designs_per_job":4,"max_mpnn_samples":4,"max_pdb_bytes_per_input":8000000,"max_rows_per_job":1,"max_rows_per_native_batch":4,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design protein binders with FoldCraft","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable Structures Dataset containing ordered trajectories, designed sequences, profile parameters, and checksum-bound structures. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"binder_designs","title":"FoldCraft binder designs"},{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified binder design structure associated with one requested trajectory.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"designed_structure","title":"FoldCraft designed structure"},{"content_schema":null,"dataset_kind":null,"description":"Per-trajectory design and filtering evidence emitted by the native workflow.","media_type":"application/json","resource_kind":"artifact","role":"design_evidence","title":"FoldCraft design evidence"},{"content_schema":null,"dataset_kind":null,"description":"The immutable native batch result with input, process, ProteinMPNN, AlphaFold lifecycle, artifact, and digest evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native FoldCraft batch result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"binder_chain":{"default":"A","pattern":"^[A-Z]$","type":"string"},"binder_hotspots":{"default":"","pattern":"^$|^[0-9]+(?:-[0-9]+)?(?:,[0-9]+(?:-[0-9]+)?)*$","type":"string"},"binder_mask":{"default":"","pattern":"^$|^[0-9]+(?:-[0-9]+)?(?:,[0-9]+(?:-[0-9]+)?)*$","type":"string"},"design_stages":{"const":"100,100,20","default":"100,100,20","type":"string"},"mpnn_samples":{"default":1,"maximum":4,"minimum":1,"type":"integer"},"mpnn_weight":{"default":"soluble","enum":["soluble","original"],"type":"string"},"num_designs":{"default":1,"maximum":4,"minimum":1,"type":"integer"},"redesign_method":{"default":"non-interface","enum":["non-interface","full"],"type":"string"},"target_chain":{"default":"A","pattern":"^[A-Z]$","type":"string"},"target_hotspots":{"pattern":"^[0-9]+(?:-[0-9]+)?(?:,[0-9]+(?:-[0-9]+)?)*$","type":"string"}},"required":["target_hotspots"],"type":"object"},"resource_class":"gpu-medium","side_effect_class":"expensive_compute","version":"0.2.0"}],"source_repository":"https://github.com/KhondamirRustamov/FoldCraft","tool_id":"foldcraft","version":"commit-pinned H100 batch profile"},{"display_name":"Genie 3","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"genie3.design_protein_structures","description":"Generate exactly one deterministic 40-residue unconditional C-alpha trace structure with the pinned Genie 3 v1 checkpoint on the H100-qualified CUDA profile. Motif scaffolding, binder design, other lengths, and multi-sample runs remain unreleased.","example":{"bindings":[],"capability_id":"genie3.design_protein_structures","parameters":{"designs":1,"direction_scale":0.8,"length":40,"mode":"unconditional","seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_pdb_bytes_per_row":2097152,"max_rows_per_job":1,"max_samples_per_row":1,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Generate an unconditional protein structure with Genie 3","outputs":[{"content_schema":null,"dataset_kind":null,"description":"An immutable, checksum-verified 40-residue C-alpha trace PDB produced by the pinned H100-qualified Genie 3 profile.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"predicted_structure","title":"Genie 3 unconditional structure"},{"content_schema":null,"dataset_kind":null,"description":"The exact validated native response with model identity, CUDA evidence, parameters, structure evidence, and result digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Genie 3 result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"designs":{"const":1,"default":1},"direction_scale":{"const":0.8,"default":0.8},"length":{"const":40,"default":40},"mode":{"const":"unconditional","default":"unconditional"},"seed":{"const":0,"default":0}},"type":"object"},"resource_class":"gpu-small","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://github.com/aqlaboratory/genie3","tool_id":"genie3","version":"v1 checkpoint release"},{"display_name":"HalluDesign","license":"Apache-2.0 source; Protenix and model-asset terms apply","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":8,"max_rows_per_native_batch":8,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"halludesign.design_protein_ligand_complexes","description":"Iteratively co-optimize protein sequence and structure with HalluDesign's permissive Protenix lane. The typed API covers starting-structure and no-PDB design, protein/context MPNN profiles, SMILES/DNA/RNA conditioning, antibody and sequence constraints, symmetry, cyclic design, inline sequence bias, and bounded native batching. AlphaFold 3 and cross-model paths are source-pruned for licensing. The released Protenix lane passed exact-image H100 qualification across starting-structure, random-ligand hybrid, and antibody-constraint surfaces with semantic and tolerance-based validation.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"id":"<value>","template_json":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"design_context"}],"capability_id":"halludesign.design_protein_ligand_complexes","parameters":{"cyclic_chain_a":false,"design_epoch_begin":0,"mpnn":"protein_mpnn","mpnn_temperature":0.1,"num_recycles":10,"num_sequences":4,"randomize_redesignable_residues":false,"ref_time_steps":50,"seed":123},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures","table","nucleotide_sequences"],"description":"One to eight checksum-bound homogeneous design rows. Each row contains a bounded Protenix template, a starting PDB or random-init specification, and optional exact SMILES/DNA/RNA conditioner values; the cohort shares scientific controls.","granularity":["selection","dataset_version"],"max_items":8,"media_types":["chemical/x-pdb","application/json","text/csv"],"min_items":1,"ordered":true,"required":true,"required_fields":["id","template_json"],"resource_kinds":["inline"],"role":"design_context","title":"Homogeneous Protenix design cohort"}],"limits":{"max_designs_per_job":32,"max_native_seconds":10800,"max_random_init_trajectories":32,"max_rows_per_job":8,"max_rows_per_native_batch":8,"max_sequence_bias_bytes":200000,"max_sequences_per_design":32,"max_template_bytes":1000000,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design and refine protein complexes with HalluDesign","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A complete typed Artifact containing ordered HalluDesign rows, sequences, structures, constraints, and native identity evidence.","media_type":"application/json","resource_kind":"artifact","role":"designed_structures","title":"HalluDesign design table"},{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified final protein-complex structure for one requested HalluDesign trajectory.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"designed_structure","title":"HalluDesign designed structure"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-bound native batch result with request, model, image, row, ligand, and artifact evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native HalluDesign result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"cdr_regions":{"maxLength":2000,"type":["string","null"]},"cyclic_chain_a":{"default":false,"type":"boolean"},"design_epoch_begin":{"default":0,"maximum":19,"minimum":0,"type":"integer"},"fixed_chains":{"maxLength":200,"type":["string","null"]},"fixed_residues":{"maxLength":4000,"type":["string","null"]},"framework_sequences":{"items":{"pattern":"^[ACDEFGHIKLMNPQRSTVWY]+$","type":"string"},"maxItems":32,"type":"array"},"mpnn":{"default":"protein_mpnn","enum":["protein_mpnn","ligand_mpnn","ligandmpnn_plus_proteinmpnn"],"type":"string"},"mpnn_temperature":{"default":0.1,"exclusiveMinimum":0,"maximum":2,"type":"number"},"num_recycles":{"default":10,"maximum":20,"minimum":2,"type":"integer"},"num_sequences":{"default":4,"maximum":32,"minimum":1,"type":"integer"},"randomize_redesignable_residues":{"default":false,"type":"boolean"},"ref_time_steps":{"default":50,"maximum":200,"minimum":1,"type":"integer"},"seed":{"default":123,"maximum":2147483647,"minimum":0,"type":"integer"},"sequence_bias_csv":{"maxLength":200000,"type":["string","null"]},"symmetry_chains":{"maxLength":200,"type":["string","null"]},"symmetry_residues":{"maxLength":4000,"type":["string","null"]},"template_for_evaluation_json":{"items":{"type":"object"},"minItems":1,"type":["array","null"]}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"0.4.0"}],"source_repository":"https://github.com/MinchaoFang/HalluDesign","tool_id":"halludesign","version":"0.4.0 pinned Protenix batch profile"},{"display_name":"HLAIIPred","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":128,"max_rows_per_native_batch":128,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"hlaiipred.predict_hla2_presentation","description":"Predict HLA-II peptide presentation probabilities and per-allele 9-mer core scores with the published two-fold HLAIIPred model. This is a presentation-risk model, not a clinical anti-drug-antibody incidence predictor.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"peptides"}],"capability_id":"hlaiipred.predict_hla2_presentation","parameters":{"alleles":[],"peptide_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version with one HLA-II peptide per row.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"peptides","title":"HLA-II peptides"}],"limits":{"max_alleles_per_row":14,"max_rows_per_job":128,"max_rows_per_native_batch":128,"max_sequence_length":30,"max_total_residues":3000,"min_sequence_length":9,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict HLA-II peptide presentation with HLAIIPred","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version with ensemble presentation probabilities and allele-specific 9-mer core scores. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"presentation_predictions","title":"HLAIIPred HLA-II presentation predictions"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-verified native response, model assets, source revision, and qualified image identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"HLAIIPred native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"alleles":{"description":"HLA-II beta-chain names or paired alpha-beta names supported by the released pseudosequence set.","items":{"minLength":5,"type":"string"},"maxItems":14,"minItems":1,"title":"HLA-II alleles","type":"array","uniqueItems":true},"peptide_column":{"default":"sequence","minLength":1,"title":"Peptide column","type":"string"}},"required":["alleles"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/pfizer-opensource/HLAIIPred","tool_id":"hlaiipred","version":"1.0.0"},{"display_name":"ImmuneBuilder","license":"BSD-3-Clause","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":100,"max_rows_per_native_batch":100,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"immunebuilder.predict_antibody_structures","description":"Predict version-pinned VH/VL antibody or VHH coordinates with ImmuneBuilder, preserving model-ensemble hashes, per-residue predicted-error semantics, sequence-conservation evidence, and immutable PDB artifacts.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"immunebuilder.predict_antibody_structures","parameters":{"heavy_chain_column":"sequence","input_mode":"auto","light_chain_column":"light_chain","numbering_scheme":"imgt","refinement":"openmm"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version with a heavy/VHH sequence and, for VH/VL mode, a paired light-chain sequence in each row.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"sequences","title":"Antibody or VHH sequences"}],"limits":{"max_output_bytes_per_role":10485760,"max_pdb_bytes":10485760,"max_rows_per_job":100,"max_rows_per_native_batch":100,"max_sequence_length":500,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict antibody and VHH structures","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A derived immutable Structures Dataset preserving every source row, explicit skipped/failed reasons, verified PDB Artifact IDs, exact model pins, sequence conservation, and ensemble-predicted error evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"predicted_structures","title":"Predicted antibody structures"},{"content_schema":null,"dataset_kind":null,"description":"The immutable terminal ImmuneBuilder batch result with stable row identities, exact request/result digests, model-weight checksums, and partial-failure evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native ImmuneBuilder evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_chain_column":{"default":"sequence","description":"Dataset column containing the heavy-chain or VHH amino-acid sequence.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy-chain or VHH column","type":"string"},"input_mode":{"default":"auto","description":"Automatically use VH/VL when a light chain is present and VHH otherwise, or require one explicit mode for every row.","enum":["auto","vhh","vh_vl"],"title":"Immune structure input mode","type":"string"},"label_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional row label column","type":["string","null"]},"light_chain_column":{"default":"light_chain","description":"Dataset column containing the light-chain amino-acid sequence when VH/VL modeling is selected or detected.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Light-chain column","type":"string"},"numbering_scheme":{"default":"imgt","enum":["imgt"],"title":"Numbering scheme","type":"string"},"refinement":{"default":"openmm","enum":["openmm"],"title":"Structure refinement","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/oxpig/ImmuneBuilder","tool_id":"immunebuilder","version":"1.2"},{"display_name":"ImmunoGeNN","license":"MIT; internal product release rights review recorded in ubi-tools","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":16,"max_rows_per_native_batch":16,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"immunogenn.score_drb1_population_risk","description":"Score protein sequences with ImmunoGeNN's global-population DRB1 pIRS model and optional exact human-reference 9-mer filtering. The released scope excludes DP, DQ, and DRB3/4/5 and is not a clinical ADA predictor.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"immunogenn.score_drb1_population_risk","parameters":{"apply_human_reference_filter":true,"sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing protein sequences to screen.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein sequences"}],"limits":{"max_rows_per_job":16,"max_rows_per_native_batch":16,"max_sequence_length":1000,"max_total_residues":5000,"min_sequence_length":15,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score global-population DRB1 presentation risk with ImmunoGeNN","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version with protein-level DRB1 pIRS sums and complete 15-mer/core evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"immunogenicity_scores","title":"ImmunoGeNN DRB1 population-risk scores"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-verified native response, human-reference identity, rights-review state, and qualified image identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"ImmunoGeNN native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"apply_human_reference_filter":{"default":true,"description":"Set pIRS and pIRS rank to zero when the selected 9-mer core occurs in the checksum-pinned human reference.","title":"Filter human-reference cores","type":"boolean"},"sequence_column":{"default":"sequence","minLength":1,"title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/novonordisk-research/ImmunoGeNN","tool_id":"immunogenn","version":"2025 workshop release"},{"display_name":"ImmunoSeq","license":"MIT; Observed Antibody Space reference data CC-BY-4.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"immunoseq.optimize_antibody_immunogenicity","description":"Rank bounded single-residue antibody substitutions with the published ImmunoSeq exact 8-12-mer objective over explicitly reviewed mutable framework positions and the frozen 2026-08-14 current-OAS snapshot. Two exact-image executions and independent reconstruction of all evaluated substitutions passed qualification.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"heavy_sequence":"<value>","heavy_sequence_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"antibody"}],"capability_id":"immunoseq.optimize_antibody_immunogenicity","parameters":{"mutable_heavy_positions":[],"mutable_light_positions":[],"top_k":20},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"One checksum-bound antibody variable-region sequence pair with explicit one-based mutable framework positions selected outside ImmunoSeq.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["heavy_sequence","heavy_sequence_sha256"],"resource_kinds":["inline"],"role":"antibody","title":"Antibody to optimize"}],"limits":{"max_mutable_positions":80,"max_rows_per_job":1,"max_sequence_length":180,"max_top_k":40,"min_rows_per_job":1,"min_sequence_length":40,"supported_alphabet":"canonical_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Rank antibody substitutions with ImmunoSeq","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Checksum-bound single-substitution candidates ranked over explicitly reviewed mutable framework positions. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"ranked_substitutions","title":"ImmunoSeq ranked substitutions"},{"content_schema":null,"dataset_kind":null,"description":"The baseline, evaluated mutation count, ranked candidates, reference-manifest identity, and exact CPU runtime provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"ImmunoSeq optimization evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"mutable_heavy_positions":{"description":"Sorted unique one-based heavy-chain framework positions reviewed by the scientist.","items":{"minimum":1,"type":"integer"},"maxItems":80,"title":"Mutable heavy-chain positions","type":"array"},"mutable_light_positions":{"description":"Sorted unique one-based light-chain framework positions reviewed by the scientist.","items":{"minimum":1,"type":"integer"},"maxItems":80,"title":"Mutable light-chain positions","type":"array"},"top_k":{"default":20,"maximum":40,"minimum":1,"title":"Ranked substitutions to retain","type":"integer"}},"required":["mutable_heavy_positions","mutable_light_positions"],"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"0.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"immunoseq.score_antibody_immunogenicity","description":"Score checksum-bound antibody variable-region sequences with the published ImmunoSeq exact 8-12-mer method against the frozen 2026-08-14 current-OAS reference snapshot. The corpus is explicitly not represented as paper-identical; its exact CPU image, all 15 filters, and independent score reconstruction passed repeat qualification.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"heavy_sequence":"<value>","heavy_sequence_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"antibodies"}],"capability_id":"immunoseq.score_antibody_immunogenicity","parameters":{"heavy_sequence_column":"heavy_sequence","light_sequence_column":"light_sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing checksum-bound heavy-chain sequences and optional checksum-bound light-chain sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["heavy_sequence","heavy_sequence_sha256"],"resource_kinds":["inline"],"role":"antibodies","title":"Antibody variable-region sequences"}],"limits":{"kmer_lengths":[8,9,10,11,12],"max_rows_per_job":1,"max_sequence_length":180,"min_rows_per_job":1,"min_sequence_length":40,"supported_alphabet":"canonical_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score antibody sequences with ImmunoSeq","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Row-preserving antibody scores with chain- and residue-level evidence from the checksum-pinned current-OAS reference snapshot. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"immunogenicity_scores","title":"ImmunoSeq antibody immunogenicity scores"},{"content_schema":null,"dataset_kind":null,"description":"The validated request, scores, reference-manifest identity, result digest, and exact CPU runtime provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"ImmunoSeq scoring evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"heavy_sequence_column":{"default":"heavy_sequence","minLength":1,"title":"Heavy-chain sequence column","type":"string"},"light_sequence_column":{"default":"light_sequence","minLength":1,"title":"Optional light-chain sequence column","type":"string"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://github.com/qj-Huang/ImmunoSeq","tool_id":"immunoseq","version":"paper-v1; current OAS snapshot 2026-08-14"},{"display_name":"ipSAE","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":25,"max_rows_per_native_batch":25,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"ipsae.score_binder_interfaces","description":"Calculate checksum-bound ipSAE v4 interface scores for a bounded cohort of predicted complexes and their per-token PAE evidence, preserving every directional chain-pair metric and structured row failure.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"pae_artifact_id":"<value>","pae_checksum_sha256":"<value>","pae_media_type":"<value>","structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"complexes"}],"capability_id":"ipsae.score_binder_interfaces","parameters":{"distance_cutoff_angstrom":10,"pae_cutoff":10},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures","comparison"],"description":"One frozen Selection or immutable Dataset Version containing a predicted complex and checksum-bound PAE Artifact for every row.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["structure_artifact_id","structure_media_type","structure_checksum_sha256","pae_artifact_id","pae_media_type","pae_checksum_sha256"],"resource_kinds":["inline"],"role":"complexes","title":"Predicted complexes and PAE evidence"}],"limits":{"max_output_bytes_per_role":50000000,"max_pae_bytes_per_job":75000000,"max_pae_bytes_per_row":25000000,"max_rows_per_job":25,"max_rows_per_native_batch":25,"max_structure_bytes_per_job":20000000,"max_structure_bytes_per_row":5000000,"min_rows_per_job":1,"supported_pae_media_types":["application/json","application/x-npz"],"supported_structure_media_types":["chemical/x-pdb","chemical/x-mmcif"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score binder interfaces with ipSAE","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset containing directional ipSAE interface evidence and explicit row failures. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"interface_scores","title":"ipSAE interface scores"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified ipSAE v4 cohort response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native ipSAE result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"distance_cutoff_angstrom":{"default":10,"maximum":30,"minimum":4,"title":"Inter-chain distance cutoff (angstrom)","type":"integer"},"pae_cutoff":{"default":10,"maximum":30,"minimum":1,"title":"PAE cutoff","type":"integer"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"4"}],"source_repository":"https://github.com/DunbrackLab/IPSAE","tool_id":"ipsae","version":"4"},{"display_name":"KA-Search","license":"BSD-3-Clause; reference-database source terms apply","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"kasearch.compare_plabdab_patent_references","description":"Find antibody-aware matches in the exact versioned PLAbDab patent reference collection using IMGT canonical positions, with independently reconstructable identity evidence and an explicit non-legal interpretation.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"kasearch.compare_plabdab_patent_references","parameters":{"chain_type_column":"antpack_chain_type","database_content_digest_sha256":"<database_content_digest_sha256>","database_id":"<database_id>","keep_best_n":5,"length_matched":false,"region":"whole","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version with an unambiguous antibody variable-region sequence and an explicit heavy/light chain classification. The governed operation searches only its named reference collection.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Classified antibody variable-region sequences"}],"limits":{"max_matches_per_row":20,"max_rows_per_job":1,"max_sequence_length":300,"min_rows_per_job":1,"supported_alphabet":"unambiguous_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Compare antibodies to PLAbDab patent references","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving annotated-sequence Dataset with ranked matches, reconstructable IMGT identity evidence, source-organism evidence, and the exact frozen PLAbDab release identity. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"patent_reference_similarity","title":"PLAbDab patent-reference similarity"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-bound native response, including the exact reference release, request, evidence, and result digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native PLAbDab patent-reference similarity result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_type_column":{"default":"antpack_chain_type","description":"Column containing H/heavy or K/L/light. Defaults to AntPack's antpack_chain_type output; legacy chain_type and other explicitly named columns remain accepted.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy/light classification column","type":"string"},"database_content_digest_sha256":{"pattern":"^[0-9a-f]{64}$","title":"Frozen reference database content digest","type":"string"},"database_id":{"maxLength":128,"minLength":1,"title":"Frozen PLAbDab patent-reference database ID","type":"string"},"keep_best_n":{"default":5,"maximum":20,"minimum":1,"title":"Top matches per antibody","type":"integer"},"label_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional candidate label column","type":["string","null"]},"length_matched":{"default":false,"title":"Require equal selected-region residue counts","type":"boolean"},"region":{"default":"whole","enum":["whole","cdrs","cdr3"],"title":"IMGT region","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Antibody sequence column","type":"string"}},"required":["database_id","database_content_digest_sha256"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"kasearch.compare_therasabdab_therapeutic_references","description":"Find antibody-aware matches in the exact versioned TheraSAbDab therapeutic reference collection using IMGT canonical positions, with independently reconstructable identity evidence and no clinical claim.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"kasearch.compare_therasabdab_therapeutic_references","parameters":{"chain_type_column":"antpack_chain_type","database_content_digest_sha256":"<database_content_digest_sha256>","database_id":"<database_id>","keep_best_n":5,"length_matched":false,"region":"whole","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version with an unambiguous antibody variable-region sequence and an explicit heavy/light chain classification. The governed operation searches only its named reference collection.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Classified antibody variable-region sequences"}],"limits":{"max_matches_per_row":20,"max_rows_per_job":1,"max_sequence_length":300,"min_rows_per_job":1,"supported_alphabet":"unambiguous_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Compare antibodies to TheraSAbDab therapeutic references","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving annotated-sequence Dataset with ranked matches, reconstructable IMGT identity evidence, and the exact frozen TheraSAbDab release identity. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"therapeutic_reference_similarity","title":"TheraSAbDab therapeutic-reference similarity"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-bound native response, including the exact reference release, request, evidence, and result digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native TheraSAbDab therapeutic-reference similarity result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_type_column":{"default":"antpack_chain_type","description":"Column containing H/heavy or K/L/light. Defaults to AntPack's antpack_chain_type output; legacy chain_type and other explicitly named columns remain accepted.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Heavy/light classification column","type":"string"},"database_content_digest_sha256":{"pattern":"^[0-9a-f]{64}$","title":"Frozen reference database content digest","type":"string"},"database_id":{"maxLength":128,"minLength":1,"title":"Frozen TheraSAbDab therapeutic-reference database ID","type":"string"},"keep_best_n":{"default":5,"maximum":20,"minimum":1,"title":"Top matches per antibody","type":"integer"},"label_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional candidate label column","type":["string","null"]},"length_matched":{"default":false,"title":"Require equal selected-region residue counts","type":"boolean"},"region":{"default":"whole","enum":["whole","cdrs","cdr3"],"title":"IMGT region","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Antibody sequence column","type":"string"}},"required":["database_id","database_content_digest_sha256"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/kovaltsuk/kasearch","tool_id":"kasearch","version":"0.1.0; reference snapshot 2026-01-03"},{"display_name":"MHC-Diff","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"mhc_diff.predict_pmhc_ensemble","description":"Generate a bounded ensemble of peptide C-alpha conformations for one checksum-bound MHC-I complex with the MHC-Diff multi-allele checkpoint. The released H100 image preserves the previously qualified scientific model behavior and passed content-identity differential qualification.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"pmhc_complex"}],"capability_id":"mhc_diff.predict_pmhc_ensemble","parameters":{"checkpoint_profile":"mhci_multi_allele_100k","num_samples":10,"sampling_steps":200,"seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One frozen Selection or immutable Structures Dataset Version containing exactly one checksum-bound PDB complex with MHC chain M and peptide chain P.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256"],"resource_kinds":["inline"],"role":"pmhc_complex","title":"MHC-I peptide complex"}],"limits":{"max_input_pdb_bytes":2097152,"max_rows_per_job":1,"max_samples":10,"min_rows_per_job":1,"supported_peptide_lengths":[8,9,10,11,12,13],"supported_sampling_steps":[200,500,1000]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict an MHC-I peptide C-alpha ensemble with MHC-Diff","outputs":[{"content_schema":null,"dataset_kind":null,"description":"One checksum-verified PDB Artifact containing the unchanged MHC and one predicted peptide C-alpha conformation.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"predicted_structure","title":"MHC-Diff peptide C-alpha ensemble structure"},{"content_schema":null,"dataset_kind":null,"description":"The exact validated native result with checkpoint, request, runtime, per-structure checksum, and peptide-coordinate evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"MHC-Diff ensemble evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"checkpoint_profile":{"const":"mhci_multi_allele_100k","default":"mhci_multi_allele_100k","description":"Checksum-pinned multi-allele MHC-I checkpoint trained on the 100K corpus.","title":"Checkpoint","type":"string"},"num_samples":{"default":10,"maximum":10,"minimum":1,"title":"Ensemble size","type":"integer"},"sampling_steps":{"default":200,"enum":[200,500,1000],"title":"Diffusion sampling steps","type":"integer"},"seed":{"default":0,"maximum":2147483647,"minimum":0,"title":"Random seed","type":"integer"}},"type":"object"},"resource_class":"gpu-small","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://github.com/X-lab-3D/MHC-Diff","tool_id":"mhc-diff","version":"0.1.0; 100K multi-allele checkpoint profile"},{"display_name":"MHCFlurry","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":512,"max_rows_per_native_batch":512,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"mhcflurry.predict_mhc1_presentation","description":"Predict MHC-I binding affinity, antigen-processing, and presentation scores for bounded peptide and allele batches using MHCFlurry 2.2.1's published presentation ensemble. These are model scores, not clinical immunogenicity outcomes.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"peptides"}],"capability_id":"mhcflurry.predict_mhc1_presentation","parameters":{"alleles":[],"include_affinity_percentile":true,"peptide_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version with one 8-15-mer peptide per row and optional paired flanks.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"peptides","title":"MHC-I peptides"}],"limits":{"max_alleles_per_job":6,"max_rows_per_job":512,"max_rows_per_native_batch":512,"max_sequence_length":15,"min_sequence_length":8,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict MHC-I presentation with MHCFlurry","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version with affinity, antigen-processing, presentation, percentile, and best-allele predictions. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"presentation_predictions","title":"MHCFlurry MHC-I presentation predictions"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-verified native response, presentation-model archive, asset manifest, and qualified image identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"MHCFlurry native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"alleles":{"description":"One to six MHC-I alleles supported by the released pan-allele model.","items":{"minLength":5,"type":"string"},"maxItems":6,"minItems":1,"title":"MHC-I alleles","type":"array","uniqueItems":true},"c_flank_column":{"default":null,"title":"C-terminal flank column","type":["string","null"]},"include_affinity_percentile":{"default":true,"title":"Include affinity percentile","type":"boolean"},"n_flank_column":{"default":null,"title":"N-terminal flank column","type":["string","null"]},"peptide_column":{"default":"sequence","minLength":1,"title":"Peptide column","type":"string"}},"required":["alleles"],"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/openvax/mhcflurry","tool_id":"mhcflurry","version":"v2.2.1 with presentation data release 2.2.0"},{"display_name":"msa","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"alignment.align_protein_sequences","description":"Align an immutable protein-sequence Dataset or Selection with pinned single-threaded MAFFT and retain complete row, gap, consensus, and variable-position evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"alignment.align_protein_sequences","parameters":{"region_label":"full_protein","sequence_column":"sequence","strategy":"auto"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing protein sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"sequences","title":"Protein sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":2000,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Align protein sequences","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Immutable equal-length aligned protein rows with exact gap, consensus, variable-position, and MAFFT provenance evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"protein_alignment","title":"Protein alignment"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified MAFFT response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native MAFFT evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"region_label":{"default":"full_protein","maxLength":100,"minLength":1,"title":"Aligned region label","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Protein sequence column","type":"string"},"strategy":{"default":"auto","enum":["auto","localpair","globalpair"],"title":"MAFFT strategy","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"alignment.align_sequences","description":"Align full sequences, exact coordinate ranges, or named antibody annotation regions with pinned MAFFT; optionally collapse exact duplicates without losing source rows or provenance.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"alignment.align_sequences","parameters":{"duplicate_policy":"keep","molecule_type":"protein","region_label":"full_sequence","region_mode":"full","sequence_column":"sequence","strategy":"auto"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","nucleotide_sequences","annotated_sequences","alignment"],"description":"A frozen Selection or immutable Dataset Version containing protein or nucleotide sequences and optional one-based region annotations.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":[],"resource_kinds":["inline"],"role":"sequences","title":"Biological sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":2000,"max_total_sequence_characters":2000000,"supported_alphabets":["protein","nucleotide"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Align protein or nucleotide sequences","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Immutable equal-length protein or nucleotide alignment rows with exact selected-region, duplicate-membership, consensus, and MAFFT provenance evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"sequence_alignment","title":"Sequence alignment"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified general MAFFT response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native MAFFT evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"allOf":[{"if":{"properties":{"region_mode":{"const":"coordinates"}},"required":["region_mode"]},"then":{"required":["region_start","region_end"]}},{"if":{"properties":{"region_mode":{"const":"annotation"}},"required":["region_mode"]},"then":{"required":["annotation_column","region_name"]}}],"properties":{"annotation_column":{"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Region annotation column","type":"string"},"duplicate_policy":{"default":"keep","enum":["keep","remove_exact"],"title":"Exact duplicate handling","type":"string"},"molecule_type":{"default":"protein","enum":["protein","nucleotide"],"title":"Molecule type","type":"string"},"region_end":{"minimum":1,"title":"One-based inclusive region end","type":"integer"},"region_label":{"default":"full_sequence","maxLength":100,"minLength":1,"title":"Region label","type":"string"},"region_mode":{"default":"full","enum":["full","coordinates","annotation"],"title":"Region selection","type":"string"},"region_name":{"maxLength":100,"minLength":1,"title":"Named annotation region","type":"string"},"region_start":{"minimum":1,"title":"One-based region start","type":"integer"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"},"strategy":{"default":"auto","enum":["auto","localpair","globalpair"],"title":"MAFFT strategy","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":2000,"max_rows_per_native_batch":2000,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_collective","successful_items_preserved":false},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"phylogeny.infer_protein_tree","description":"Infer an approximate maximum-likelihood protein phylogeny from an immutable equal-length alignment with pinned FastTree, explicit substitution/support methods, exact leaf conservation, normalized topology, and canonical Newick evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"protein_aligned_sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"phylogeny.infer_protein_tree","parameters":{"aligned_sequence_column":"protein_aligned_sequence","substitution_model":"jtt","support":"sh_like"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["alignment"],"description":"A frozen Selection or immutable ALIGNMENT Dataset Version containing equal-length gapped protein sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["protein_aligned_sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Aligned protein sequences"}],"limits":{"max_alignment_length":5000,"max_rows_per_job":2000,"max_rows_per_native_batch":2000,"min_rows_per_job":3,"supported_alphabet":"aligned_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Infer protein phylogeny","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Normalized tree nodes with parent, source leaf, branch length, SH-like support, depth, descendant count, model, and digest evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"protein_phylogeny","title":"Protein phylogeny"},{"content_schema":null,"dataset_kind":null,"description":"Canonical Newick using quoted original immutable row identities.","media_type":"text/x-newick","resource_kind":"artifact","role":"phylogeny_newick","title":"Canonical Newick"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified FastTree response and synthetic transport tree.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native FastTree evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"aligned_sequence_column":{"default":"protein_aligned_sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Aligned protein column","type":"string"},"substitution_model":{"default":"jtt","enum":["jtt","wag"],"title":"Protein substitution model","type":"string"},"support":{"default":"sh_like","description":"SH-like local support is not a bootstrap probability.","enum":["sh_like","none"],"title":"Local branch support","type":"string"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"msa","version":null},{"display_name":"Nanobody Polyreactivity","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":100,"max_rows_per_native_batch":100,"mode":"native_batch","native_batch_unit":"groups","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"nanobody_polyreactivity.score_nanobody_sequences","description":"Score heavy-chain-only nanobody variable domains with the Harvey et al. original- and deep-FACS one-hot logistic models and report CDR biochemical descriptors.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"nanobody_polyreactivity.score_nanobody_sequences","parameters":{"sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing heavy-chain-only nanobody variable-domain amino-acid sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Nanobody sequences"}],"limits":{"deep_model_feature_count":800,"max_rows_per_job":100,"max_sequence_length":200,"min_sequence_length":80,"original_model_feature_count":780,"supported_alphabet":"unambiguous_protein","supported_cdr1_length":8,"supported_cdr2_lengths":[8,9],"supported_cdr3_length_range":[6,22],"supported_chain_type":"heavy_chain_only_nanobody_variable_domain"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Score nanobody polyreactivity","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving typed result Artifact with both published decision scores, CDR evidence, biochemical descriptors, model identity, and provenance. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"polyreactivity_scores","title":"Nanobody polyreactivity scores"},{"content_schema":null,"dataset_kind":null,"description":"The independently verified native response with request, model-bundle, scientific-result, and row evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Nanobody polyreactivity native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"sequence_column":{"default":"sequence","description":"Dataset column containing heavy-chain-only nanobody variable-domain amino-acid sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/debbiemarkslab/nanobody-polyreactivity","tool_id":"nanobody-polyreactivity","version":"Harvey et al. 2022 release"},{"display_name":"NbForge","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"nbforge.predict_nanobody_structures","description":"Predict checksum-bound nanobody structures with the pinned deterministic NbForge CPU checkpoint, conserving every submitted VHH sequence and returning independently validated PDB geometry and confidence evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"nbforge.predict_nanobody_structures","parameters":{"minimize":false,"nbframe":false,"seed":1,"sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"Exact immutable input bound by the canonical Run.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Nanobody sequences"}],"limits":{"max_pdb_bytes_per_job":4194304,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":1,"max_sequence_length":180,"min_rows_per_job":1,"min_sequence_length":80,"supported_alphabet":"unambiguous_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict nanobody structures with NbForge","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A child Dataset Version retaining source rows, immutable PDB Artifact bindings, confidence, and checksum evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"predicted_structures","title":"NbForge predicted structures"},{"content_schema":null,"dataset_kind":null,"description":"An immutable sequence-conserving NbForge PDB output.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"predicted_structure_pdb","title":"Predicted nanobody PDB"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-bound NbForge native response.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native NbForge result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"minimize":{"const":false,"default":false,"type":"boolean"},"nbframe":{"const":false,"default":false,"type":"boolean"},"seed":{"const":1,"default":1,"type":"integer"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Nanobody sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://gitlab.doc.ic.ac.uk/sormanni-lab/nbforge","tool_id":"nbforge","version":"pinned 2026 release profile"},{"display_name":"ngs","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"ngs.collapse_umi_duplicates","description":"Collapse reads only when exact named UMI values and configurable global sequence identity both match, retain deterministic highest-quality representatives, and emit complete membership evidence.","example":{"bindings":[{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"umi_reads"}],"capability_id":"ngs.collapse_umi_duplicates","parameters":{"representative_policy":"highest_mean_quality","sequence_identity_threshold":0.97,"sequence_match_policy":"global_edit_identity","umi_match_policy":"exact_named_segments","unprocessed_policy":"retain_as_singleton"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":[],"description":"Immutable gzip NDJSON evidence emitted by ngs.trim_umi, including named UMI values, per-read sequence quality, and source ordinals.","granularity":["asset"],"max_items":1,"media_types":["application/gzip","application/x-gzip"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"umi_reads","title":"UMI-trimmed read evidence"}],"limits":{"max_input_bytes_per_file":1099511627776,"max_input_files":1,"max_output_bytes_per_role":1099511627776},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Collapse UMI-supported PCR duplicates","outputs":[{"content_schema":null,"dataset_kind":"reads","description":"Queryable READS Dataset Version containing deterministic highest-quality representatives, group sizes, duplicate counts, named UMI evidence, and explicit passthrough reads.","media_type":null,"resource_kind":"dataset_version","role":"collapsed_reads_dataset","title":"UMI-collapsed reads"},{"content_schema":null,"dataset_kind":null,"description":"Immutable deterministic gzip NDJSON containing each retained representative or passthrough read and its exact collapse-group evidence.","media_type":"application/gzip","resource_kind":"asset","role":"collapsed_reads","title":"Collapsed read evidence"},{"content_schema":null,"dataset_kind":null,"description":"One immutable membership row per input read with representative identity, exact named UMIs, sequence identity, role, and passthrough reason.","media_type":"application/gzip","resource_kind":"asset","role":"duplicate_membership","title":"Duplicate membership evidence"},{"content_schema":null,"dataset_kind":null,"description":"Exact input/output conservation, eligible and passthrough counts, collapsed duplicates, group sizes, comparisons, parameters, and execution evidence.","media_type":"application/json","resource_kind":"artifact","role":"collapse_metrics","title":"Duplicate-collapse metrics"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"representative_policy":{"default":"highest_mean_quality","description":"Choose the read with the highest mean Phred score, then the earliest source ordinal, as the deterministic representative.","enum":["highest_mean_quality"],"title":"Representative policy","type":"string"},"sequence_identity_threshold":{"default":0.97,"description":"Minimum normalized global edit identity required in addition to exact UMI equality.","maximum":1.0,"minimum":0.5,"title":"Minimum sequence identity","type":"number"},"sequence_match_policy":{"default":"global_edit_identity","description":"Compare trimmed sequences with global Levenshtein edit identity normalized by the longer sequence.","enum":["global_edit_identity"],"title":"Sequence match policy","type":"string"},"umi_match_policy":{"default":"exact_named_segments","description":"Require equality of every named UMI segment; reads with different segment names or values never collapse.","enum":["exact_named_segments"],"title":"UMI match policy","type":"string"},"unprocessed_policy":{"default":"retain_as_singleton","description":"Retain every read without usable UMI evidence as an explicit singleton rather than discarding it.","enum":["retain_as_singleton"],"title":"Reads without usable UMI","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"ngs.demultiplex_reads","description":"Assign immutable FASTQ reads to samples using an explicit 5-prime adapter/barcode policy while retaining ambiguous and unmatched records.","example":{"bindings":[{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"reads"}],"capability_id":"ngs.demultiplex_reads","parameters":{"barcodes":[],"match_policy":"unique_best_hamming","mismatch_tolerance":0,"trim_matched_prefix":true},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":[],"description":"One immutable FASTQ or FASTQ.GZ Asset, including a merged-read Asset emitted by the paired-read capability.","granularity":["asset"],"max_items":1,"media_types":["application/fastq","text/fastq","application/gzip","application/x-gzip"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"reads","title":"Reads to demultiplex"}],"limits":{"max_input_bytes_per_file":1099511627776,"max_input_files":1,"max_output_bytes_per_role":1099511627776},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Demultiplex FASTQ reads","outputs":[{"content_schema":null,"dataset_kind":null,"description":"One deterministic gzip FASTQ Asset for each non-empty configured sample, suitable for direct Pipeline fan-out into UMI extraction.","media_type":"application/gzip","resource_kind":"asset","role":"sample_reads_fastq","title":"Per-sample FASTQ"},{"content_schema":null,"dataset_kind":null,"description":"A deterministic gzip FASTQ Asset for non-empty unassigned reads, retained for review or explicit downstream processing.","media_type":"application/gzip","resource_kind":"asset","role":"unassigned_reads_fastq","title":"Unassigned FASTQ"},{"content_schema":null,"dataset_kind":"reads","description":"One queryable READS Dataset Version per configured sample, retaining barcode, mismatch, trim, and raw-record lineage.","media_type":null,"resource_kind":"dataset_version","role":"sample_reads","title":"Per-sample reads"},{"content_schema":null,"dataset_kind":"reads","description":"Queryable READS Dataset Version containing no-match, ambiguous, and too-short reads with structured reasons.","media_type":null,"resource_kind":"dataset_version","role":"unassigned_reads","title":"Unassigned reads"},{"content_schema":null,"dataset_kind":null,"description":"Immutable gzip-compressed NDJSON assignment stream used to reproduce all child Datasets.","media_type":"application/gzip","resource_kind":"asset","role":"assignments","title":"Demultiplex assignments"},{"content_schema":null,"dataset_kind":null,"description":"Exact assignment conservation, per-sample yield, unassigned reasons, parameters, and execution evidence.","media_type":"application/json","resource_kind":"artifact","role":"demultiplex_metrics","title":"Demultiplex metrics"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"barcodes":{"description":"Unique sample identifiers and equal-length 5-prime adapter/barcode prefixes.","items":{"additionalProperties":false,"properties":{"adapter":{"default":"","pattern":"^[ACGTacgt]{0,128}$","type":"string"},"barcode":{"pattern":"^[ACGTacgt]{1,64}$","type":"string"},"sample_id":{"pattern":"^[A-Za-z0-9][A-Za-z0-9_.-]{0,99}$","type":"string"}},"required":["sample_id","barcode"],"type":"object"},"maxItems":384,"minItems":1,"title":"Sample barcodes","type":"array"},"match_policy":{"default":"unique_best_hamming","description":"Assign only a unique lowest-distance prefix; retain equal-best ties as ambiguous and unassigned.","enum":["unique_best_hamming"],"title":"Match policy","type":"string"},"mismatch_tolerance":{"default":0,"description":"Maximum Hamming distance from a configured 5-prime prefix.","maximum":3,"minimum":0,"title":"Mismatch tolerance","type":"integer"},"trim_matched_prefix":{"default":true,"description":"Remove the configured adapter and barcode prefix from assigned read sequence and quality while retaining trim metadata.","title":"Trim matched prefix","type":"boolean"}},"required":["barcodes"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"ngs.merge_paired_reads","description":"Merge immutable paired-end FASTQ Assets with FLASH while preserving merged, unmerged-forward, unmerged-reverse, metrics, and execution evidence.","example":{"bindings":[{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"reads_r1"},{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"reads_r2"}],"capability_id":"ngs.merge_paired_reads","parameters":{"allow_outies":false,"max_overlap":300,"min_overlap":10,"mismatch_density":0.25},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":[],"description":"An immutable forward-read FASTQ or FASTQ.GZ Asset.","granularity":["asset"],"max_items":1,"media_types":["application/fastq","text/fastq","application/gzip","application/x-gzip"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"reads_r1","title":"Forward reads (R1)"},{"dataset_kinds":[],"description":"The immutable reverse-read FASTQ or FASTQ.GZ Asset paired with R1.","granularity":["asset"],"max_items":1,"media_types":["application/fastq","text/fastq","application/gzip","application/x-gzip"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"reads_r2","title":"Reverse reads (R2)"}],"limits":{"max_input_bytes_per_file":1099511627776,"max_input_files":2,"max_output_bytes_per_role":1099511627776},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Merge paired FASTQ reads","outputs":[{"content_schema":null,"dataset_kind":"reads","description":"Queryable READS Dataset Version containing successfully merged pairs with per-base Phred quality; its immutable FASTQ source Asset is retained.","media_type":null,"resource_kind":"dataset_version","role":"merged_reads","title":"Merged reads"},{"content_schema":null,"dataset_kind":"reads","description":"Queryable READS Dataset Version preserving unmerged R1 reads with per-base Phred quality; its immutable FASTQ source Asset is retained.","media_type":null,"resource_kind":"dataset_version","role":"unmerged_forward","title":"Unmerged forward reads"},{"content_schema":null,"dataset_kind":"reads","description":"Queryable READS Dataset Version preserving unmerged R2 reads with per-base Phred quality; its immutable FASTQ source Asset is retained.","media_type":null,"resource_kind":"dataset_version","role":"unmerged_reverse","title":"Unmerged reverse reads"},{"content_schema":null,"dataset_kind":null,"description":"Immutable merged-read FASTQ suitable as direct input to downstream NGS Pipeline steps.","media_type":"application/fastq","resource_kind":"asset","role":"merged_reads_fastq","title":"Merged reads FASTQ"},{"content_schema":null,"dataset_kind":null,"description":"Immutable unmerged forward-read FASTQ suitable for explicit downstream processing.","media_type":"application/fastq","resource_kind":"asset","role":"unmerged_forward_fastq","title":"Unmerged forward FASTQ"},{"content_schema":null,"dataset_kind":null,"description":"Immutable unmerged reverse-read FASTQ suitable for explicit downstream processing.","media_type":"application/fastq","resource_kind":"asset","role":"unmerged_reverse_fastq","title":"Unmerged reverse FASTQ"},{"content_schema":null,"dataset_kind":null,"description":"Immutable merge counts, rate, parameters, and native execution evidence.","media_type":"application/json","resource_kind":"artifact","role":"merge_metrics","title":"Merge metrics"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"allow_outies":{"default":false,"description":"Allow outward-facing paired-end orientation in addition to the standard innie orientation.","title":"Allow outie orientation","type":"boolean"},"max_overlap":{"default":300,"description":"Maximum nucleotide overlap considered by FLASH and required to be at least the minimum overlap.","maximum":1000,"minimum":10,"title":"Maximum overlap","type":"integer"},"min_overlap":{"default":10,"description":"Minimum nucleotide overlap required to merge a pair.","maximum":300,"minimum":5,"title":"Minimum overlap","type":"integer"},"mismatch_density":{"default":0.25,"description":"Maximum fraction of mismatched bases allowed in the overlap.","maximum":1,"minimum":0,"title":"Maximum mismatch density","type":"number"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"2.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"ngs.trim_umi","description":"Extract one or more named 5-prime or 3-prime UMI segments from immutable FASTQ reads, retain UMI sequence and Phred evidence, and trim only the declared ranges.","example":{"bindings":[{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"reads"}],"capability_id":"ngs.trim_umi","parameters":{"extraction_policy":"exact_segments","segments":[],"trim_umi_bases":true},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":[],"description":"One immutable FASTQ or FASTQ.GZ Asset. Pipeline inputs may be merged reads or a sample-specific FASTQ emitted by demultiplexing.","granularity":["asset"],"max_items":1,"media_types":["application/fastq","text/fastq","application/gzip","application/x-gzip"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"reads","title":"Reads with UMI bases"}],"limits":{"max_input_bytes_per_file":1099511627776,"max_input_files":1,"max_output_bytes_per_role":1099511627776},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Extract and trim UMI segments","outputs":[{"content_schema":null,"dataset_kind":"reads","description":"Queryable READS Dataset Version retaining named UMI sequences, UMI Phred evidence, exact trim ranges, source record identity, and explicit unprocessed reasons.","media_type":null,"resource_kind":"dataset_version","role":"trimmed_reads_dataset","title":"UMI-trimmed reads"},{"content_schema":null,"dataset_kind":null,"description":"Immutable deterministic gzip NDJSON containing every processed or unprocessed read and its exact UMI evidence.","media_type":"application/gzip","resource_kind":"asset","role":"trimmed_reads","title":"UMI-trimmed read evidence"},{"content_schema":null,"dataset_kind":null,"description":"Exact conservation, processed/unprocessed reasons, segment quality summaries, trim counts, frozen parameters, and execution evidence.","media_type":"application/json","resource_kind":"artifact","role":"umi_metrics","title":"UMI extraction metrics"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"extraction_policy":{"default":"exact_segments","description":"Use the exact named segment ranges; short or per-read overlapping ranges remain explicit unprocessed records.","enum":["exact_segments"],"title":"Extraction policy","type":"string"},"segments":{"description":"Named, non-overlapping UMI ranges measured inward from the selected read end. Offset bases are retained unless covered by another segment.","items":{"additionalProperties":false,"properties":{"end":{"default":"five_prime","enum":["five_prime","three_prime"],"type":"string"},"length":{"maximum":64,"minimum":1,"type":"integer"},"name":{"pattern":"^[A-Za-z][A-Za-z0-9_.-]{0,63}$","type":"string"},"offset":{"default":0,"maximum":128,"minimum":0,"type":"integer"}},"required":["name","end","length"],"type":"object"},"maxItems":4,"minItems":1,"title":"UMI segments","type":"array"},"trim_umi_bases":{"default":true,"description":"Remove only declared UMI ranges from sequence and quality while retaining exact UMI and trim metadata.","title":"Trim UMI bases","type":"boolean"}},"required":["segments"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"ngs","version":null},{"display_name":"OpenDDE","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":4,"max_rows_per_native_batch":4,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"opendde.predict_complex_structure","description":"Predict an all-atom protein, antibody–antigen, nucleic-acid, ligand, or ion complex with selectable bounded OpenDDE inference settings.","example":{"bindings":[],"capability_id":"opendde.predict_complex_structure","parameters":{"checkpoint_variant":"general","deterministic":true,"diffusion_steps":200,"dtype":"fp32","jobs":[],"pairformer_cycles":10,"samples":1,"seed":101},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_a3m_records_per_entity":10000,"max_covalent_bonds":64,"max_entities":8,"max_entity_copies":4,"max_inline_a3m_bytes_per_entity":2000000,"max_output_bytes_per_role":104857600,"max_polymer_tokens":512,"max_rows_per_job":4,"max_rows_per_native_batch":4},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict biomolecular complex structure","outputs":[{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified predicted complex for one requested batch row and sample.","media_type":"chemical/x-mmcif","resource_kind":"artifact","role":"predicted_structure","title":"OpenDDE predicted complex"},{"content_schema":null,"dataset_kind":null,"description":"The immutable native batch result with per-row confidence, request, model, CUDA, structure, and checksum evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native OpenDDE result"}],"parameters_schema":{"$defs":{"CovalentBond":{"additionalProperties":false,"properties":{"atom1":{"anyOf":[{"pattern":"^[A-Za-z0-9'\\\"*+.-]{1,8}$","type":"string"},{"minimum":1,"type":"integer"}],"title":"Atom1"},"atom2":{"anyOf":[{"pattern":"^[A-Za-z0-9'\\\"*+.-]{1,8}$","type":"string"},{"minimum":1,"type":"integer"}],"title":"Atom2"},"copy1":{"default":1,"maximum":4,"minimum":1,"title":"Copy1","type":"integer"},"copy2":{"default":1,"maximum":4,"minimum":1,"title":"Copy2","type":"integer"},"entity1":{"pattern":"^[1-9][0-9]*$","title":"Entity1","type":"string"},"entity2":{"pattern":"^[1-9][0-9]*$","title":"Entity2","type":"string"},"position1":{"pattern":"^[1-9][0-9]*$","title":"Position1","type":"string"},"position2":{"pattern":"^[1-9][0-9]*$","title":"Position2","type":"string"}},"required":["entity1","position1","atom1","entity2","position2","atom2"],"title":"CovalentBond","type":"object"},"DNASequence":{"additionalProperties":false,"description":"Single-stranded DNA using A, C, G, T, N, or X.","properties":{"count":{"default":1,"maximum":4,"minimum":1,"title":"Count","type":"integer"},"id":{"anyOf":[{"items":{"pattern":"^[A-Za-z][A-Za-z0-9]{0,3}$","type":"string"},"maxItems":4,"minItems":1,"type":"array","uniqueItems":true},{"type":"null"}],"default":null,"title":"Id"},"modifications":{"items":{"$ref":"#/$defs/NucleicModification"},"maxItems":64,"title":"Modifications","type":"array"},"sequence":{"maxLength":512,"minLength":1,"pattern":"^[ACGTNXacgtnx]+$","title":"Sequence","type":"string"}},"required":["sequence"],"title":"DNASequence","type":"object"},"Entity":{"additionalProperties":false,"description":"Exactly one of proteinChain, dnaSequence, rnaSequence, ligand, or ion.","oneOf":[{"required":["proteinChain"]},{"required":["dnaSequence"]},{"required":["rnaSequence"]},{"required":["ligand"]},{"required":["ion"]}],"properties":{"dnaSequence":{"anyOf":[{"$ref":"#/$defs/DNASequence"},{"type":"null"}],"default":null},"ion":{"anyOf":[{"$ref":"#/$defs/Ion"},{"type":"null"}],"default":null},"ligand":{"anyOf":[{"$ref":"#/$defs/Ligand"},{"type":"null"}],"default":null},"proteinChain":{"anyOf":[{"$ref":"#/$defs/ProteinChain"},{"type":"null"}],"default":null},"rnaSequence":{"anyOf":[{"$ref":"#/$defs/RNASequence"},{"type":"null"}],"default":null}},"title":"Entity","type":"object"},"Ion":{"additionalProperties":false,"properties":{"count":{"default":1,"maximum":4,"minimum":1,"title":"Count","type":"integer"},"id":{"anyOf":[{"items":{"pattern":"^[A-Za-z][A-Za-z0-9]{0,3}$","type":"string"},"maxItems":4,"minItems":1,"type":"array","uniqueItems":true},{"type":"null"}],"default":null,"title":"Id"},"ion":{"description":"A CCD ion component name without the CCD_ prefix.","maxLength":8,"pattern":"^[A-Za-z][A-Za-z0-9]{0,7}$","title":"Ion","type":"string"}},"required":["ion"],"title":"Ion","type":"object"},"Ligand":{"additionalProperties":false,"properties":{"count":{"default":1,"maximum":4,"minimum":1,"title":"Count","type":"integer"},"id":{"anyOf":[{"items":{"pattern":"^[A-Za-z][A-Za-z0-9]{0,3}$","type":"string"},"maxItems":4,"minItems":1,"type":"array","uniqueItems":true},{"type":"null"}],"default":null,"title":"Id"},"ligand":{"description":"A CCD_ component expression or a bounded single-token SMILES. FILE_ inputs are disabled.","maxLength":512,"minLength":1,"title":"Ligand","type":"string"}},"required":["ligand"],"title":"Ligand","type":"object"},"NucleicModification":{"additionalProperties":false,"properties":{"basePosition":{"minimum":1,"title":"Baseposition","type":"integer"},"modificationType":{"pattern":"^CCD_[A-Z0-9]{1,8}$","title":"Modificationtype","type":"string"}},"required":["modificationType","basePosition"],"title":"NucleicModification","type":"object"},"OpenDDEJob":{"additionalProperties":false,"properties":{"covalent_bonds":{"items":{"$ref":"#/$defs/CovalentBond"},"maxItems":64,"title":"Covalent Bonds","type":"array"},"modelSeeds":{"anyOf":[{"items":{"maximum":2147483647,"minimum":0,"type":"integer"},"maxItems":1,"minItems":1,"type":"array"},{"type":"null"}],"default":null,"title":"Modelseeds"},"name":{"default":"prediction","pattern":"^[A-Za-z0-9][A-Za-z0-9_-]{0,63}$","title":"Name","type":"string"},"sequences":{"items":{"$ref":"#/$defs/Entity"},"maxItems":8,"minItems":1,"title":"Sequences","type":"array"}},"required":["sequences"],"title":"OpenDDEJob","type":"object"},"ProteinChain":{"additionalProperties":false,"description":"Protein chain using the 20 standard amino acids or X.","properties":{"count":{"default":1,"maximum":4,"minimum":1,"title":"Count","type":"integer"},"id":{"anyOf":[{"items":{"pattern":"^[A-Za-z][A-Za-z0-9]{0,3}$","type":"string"},"maxItems":4,"minItems":1,"type":"array","uniqueItems":true},{"type":"null"}],"default":null,"title":"Id"},"modifications":{"items":{"$ref":"#/$defs/ProteinModification"},"maxItems":64,"title":"Modifications","type":"array"},"pairedMsa":{"anyOf":[{"maxLength":2000000,"type":"string"},{"type":"null"}],"default":null,"description":"Optional inline A3M; the first record must exactly match this chain.","title":"Pairedmsa"},"sequence":{"maxLength":512,"minLength":1,"pattern":"^[ACDEFGHIKLMNPQRSTVWYXacdefghiklmnpqrstvwyx]+$","title":"Sequence","type":"string"},"unpairedMsa":{"anyOf":[{"maxLength":2000000,"type":"string"},{"type":"null"}],"default":null,"description":"Optional inline A3M; the first record must exactly match this chain.","title":"Unpairedmsa"}},"required":["sequence"],"title":"ProteinChain","type":"object"},"ProteinModification":{"additionalProperties":false,"properties":{"ptmPosition":{"minimum":1,"title":"Ptmposition","type":"integer"},"ptmType":{"pattern":"^CCD_[A-Z0-9]{1,8}$","title":"Ptmtype","type":"string"}},"required":["ptmType","ptmPosition"],"title":"ProteinModification","type":"object"},"RNASequence":{"additionalProperties":false,"description":"Single-stranded RNA using A, C, G, U, N, or X.","properties":{"count":{"default":1,"maximum":4,"minimum":1,"title":"Count","type":"integer"},"id":{"anyOf":[{"items":{"pattern":"^[A-Za-z][A-Za-z0-9]{0,3}$","type":"string"},"maxItems":4,"minItems":1,"type":"array","uniqueItems":true},{"type":"null"}],"default":null,"title":"Id"},"modifications":{"items":{"$ref":"#/$defs/NucleicModification"},"maxItems":64,"title":"Modifications","type":"array"},"sequence":{"maxLength":512,"minLength":1,"pattern":"^[ACGUNXacgunx]+$","title":"Sequence","type":"string"},"unpairedMsa":{"anyOf":[{"maxLength":2000000,"type":"string"},{"type":"null"}],"default":null,"description":"Optional inline RNA A3M; the first record must exactly match this chain.","title":"Unpairedmsa"}},"required":["sequence"],"title":"RNASequence","type":"object"}},"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"description":"One to four bounded AlphaFold-Server-style complexes processed sequentially in one native model-loading process. Inputs are inline values; client filesystem paths and templates are not accepted. Each complex uses the shared execution profile and the compute budget requires samples × diffusion_steps × pairformer_cycles <= 2000 per complex.","properties":{"checkpoint_variant":{"default":"general","description":"general supports mixed biomolecular complexes; antibody_antigen requires at least two protein chains.","enum":["general","antibody_antigen"],"title":"Checkpoint Variant","type":"string"},"deterministic":{"default":true,"description":"Use deterministic PyTorch algorithms. Deterministic runs can reuse an exact cache entry.","title":"Deterministic","type":"boolean"},"diffusion_steps":{"default":200,"description":"100 or 200 diffusion steps.","enum":[100,200],"title":"Diffusion Steps","type":"integer"},"dtype":{"default":"fp32","description":"FP32 or BF16 numerical precision.","enum":["fp32","bf16"],"title":"Dtype","type":"string"},"jobs":{"description":"One to four uniquely named complexes evaluated sequentially inside one native OpenDDE process so model loading is amortized without concurrent GPU inference.","items":{"$ref":"#/$defs/OpenDDEJob"},"maxItems":4,"minItems":1,"title":"Jobs","type":"array"},"pairformer_cycles":{"default":10,"description":"Five or ten Pairformer cycles.","enum":[5,10],"title":"Pairformer Cycles","type":"integer"},"samples":{"default":1,"description":"One or two candidate structures.","enum":[1,2],"title":"Samples","type":"integer"},"seed":{"default":101,"maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"}},"required":["jobs"],"title":"OpenDDE complex prediction parameters","type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"1.3.0"}],"source_repository":"https://github.com/aurekaresearch/OpenDDE","tool_id":"opendde","version":"1.0.2 pinned CUDA/H100 profile"},{"display_name":"PALM","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":32,"max_rows_per_native_batch":32,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"palm.predict_aggregation_profiles","description":"Predict sequence-level amyloid aggregation propensity and residue-level candidate aggregation-prone regions with the checksum-bound five-fold PALM ensemble on the exact qualified CPU image.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"palm.predict_aggregation_profiles","parameters":{"model_variant":"PALM","residue_threshold":0.5,"sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing canonical amino-acid sequences for aggregation screening.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein or peptide sequences"}],"limits":{"max_native_batch_size":32,"max_rows_per_job":32,"max_sequence_length":1022,"max_total_residues":4096,"min_rows_per_job":1,"supported_alphabet":"20_canonical_amino_acids"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict peptide aggregation profiles with PALM","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version with sequence and residue scores, candidate regions, fold evidence, and immutable lineage. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"aggregation_profiles","title":"PALM aggregation profiles"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-verified native response and exact staged-asset identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"PALM native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"model_variant":{"default":"PALM","description":"PALM is trained on padded WaltzDB; PALM_NNK and PALM_NNK_OH are trained on the larger NNK1-3 assay dataset.","enum":["PALM","PALM_NNK","PALM_NNK_OH"],"title":"PALM model variant","type":"string"},"residue_threshold":{"default":0.5,"description":"Screening threshold used to report contiguous candidate regions; not a universally calibrated amyloid classification cutoff.","maximum":1.0,"minimum":0.0,"title":"Residue screening threshold","type":"number"},"sequence_column":{"default":"sequence","description":"Dataset column containing canonical amino-acid sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://github.com/novonordisk-research/PALM","tool_id":"palm","version":"v1.2.0"},{"display_name":"pkpd","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":false,"released":true,"status":"unavailable","unavailability_category":"model_binding","unavailable_reason":"no_qualified_public_model_binding"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"pkpd.fit_data","description":"Estimate a bounded set of parameters for a fit-qualified, version-pinned PK/PD or QSP model from scientist-supplied observations using the deterministic native fitting workflow.","example":{"bindings":[],"capability_id":"pkpd.fit_data","parameters":{"backend":"<backend>","base_scenario_id":"<base_scenario_id>","model_id":"<model_id>","model_version":"<model_version>","observed_data":[],"optimizer_options":{"max_iterations":1},"parameters_to_fit":{"CL_L_day":{"bounds":[],"initial":1.0}}},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_observed_rows":500,"max_optimizer_iterations":80,"max_parameters_to_fit":1,"max_published_rows":100000,"max_trajectory_columns":489,"max_trajectory_rows":100000,"released_backend":"sciml_deterministic","released_base_scenario_id":"fig3_5mgkg_q2w_70kg_dynamic","released_model_id":"panoilia_2015_bevacizumab_vegf165_qss_tmdd","released_model_version":"0.3.0"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Fit qualified PK/PD model parameters","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The complete estimated parameters, objective improvement, fitted trajectory, optimizer diagnostics, and immutable execution provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Fitting result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"backend":{"const":"sciml_deterministic","title":"Qualified fitting method","type":"string"},"base_scenario_id":{"const":"fig3_5mgkg_q2w_70kg_dynamic","description":"Released 5 mg/kg every-two-weeks regimen.","title":"Starting configuration","type":"string"},"model_id":{"const":"panoilia_2015_bevacizumab_vegf165_qss_tmdd","description":"The one immutable PK/PD model release qualified for this fitting question.","title":"Model ID","type":"string"},"model_version":{"const":"0.3.0","description":"Exact immutable model-package version qualified for fitting.","title":"Model version","type":"string"},"observed_data":{"allOf":[{"contains":{"properties":{"time":{"const":0}},"required":["time"],"type":"object"},"maxContains":1,"minContains":1},{"contains":{"properties":{"time":{"const":42}},"required":["time"],"type":"object"},"maxContains":1,"minContains":1}],"description":"Time in days and total bevacizumab concentration in mg/L for the released apparent-clearance question. Rows must be strictly time-ordered by the native API and include both day 0 and day 42.","items":{"additionalProperties":false,"properties":{"time":{"description":"Elapsed time in days.","maximum":42,"minimum":0,"title":"Time","type":"number"},"total_bevacizumab_mg_L":{"description":"Measured total bevacizumab concentration in mg/L.","title":"Total bevacizumab concentration","type":"number"}},"required":["time","total_bevacizumab_mg_L"],"type":"object"},"maxItems":500,"minItems":8,"title":"Total bevacizumab observations","type":"array","uniqueItems":true},"optimizer_options":{"additionalProperties":false,"properties":{"max_iterations":{"const":80,"type":"integer"}},"required":["max_iterations"],"title":"Bounded optimizer controls","type":"object"},"parameters_to_fit":{"additionalProperties":false,"maxProperties":1,"minProperties":1,"properties":{"CL_L_day":{"additionalProperties":false,"description":"Apparent clearance in L/day; the released initial value and bounds are fixed.","properties":{"bounds":{"items":false,"maxItems":2,"minItems":2,"prefixItems":[{"const":0.03,"type":"number"},{"const":0.8,"type":"number"}],"type":"array"},"initial":{"const":0.12,"type":"number"}},"required":["initial","bounds"],"title":"Apparent bevacizumab clearance","type":"object"}},"required":["CL_L_day"],"title":"Apparent clearance to estimate","type":"object"}},"required":["model_id","model_version","base_scenario_id","backend","observed_data","parameters_to_fit","optimizer_options"],"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"pkpd.fit_user_model","description":"Estimate selected parameters of an immutable, validated user-owned PK/PD or QSP model from bounded observed time-series data.","example":{"bindings":[],"capability_id":"pkpd.fit_user_model","parameters":{"backend":"<backend>","data_mapping":{"duplicate_policy":"reject","mapping_version":1,"missing_value_policy":"reject","time":"time"},"dosing_regimen":{"doses":[]},"initial_states":{},"model_version_id":"<model_version_id>","nlme_options":{"inner_max_iterations":1,"method":"<method>"},"observable_column":"<observable_column>","observed_data":[],"optimizer_options":{},"parameters":{},"parameters_to_fit":{},"solver_options":{},"time_column":"<time_column>","time_span":{"end":1.0,"start":1.0,"step":1.0},"value_column":"<value_column>"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_observed_rows":500,"max_optimizer_iterations":80,"max_parameters_to_fit":8,"max_population_inner_iterations":80,"max_published_rows":100000,"max_trajectory_columns":489,"max_trajectory_rows":100000,"qualified_population_backends":["population_focei"],"released_backend":"sciml_deterministic","released_backends":["sciml_deterministic","population_focei"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Fit data to a private PK/PD model","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The complete fitted parameters, objective improvement, trajectory arrays, diagnostics, and immutable execution provenance for the private model.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Private-model fitting result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"allOf":[{"if":{"properties":{"backend":{"const":"population_focei"}},"required":["backend"]},"then":{"properties":{"observed_data":{"items":{"required":["subject_id"]}}},"required":["nlme_options","subject_id_column"]}}],"properties":{"backend":{"enum":["sciml_deterministic","population_focei"],"type":"string"},"covariates":{"additionalProperties":{"additionalProperties":false,"oneOf":[{"required":["value"]},{"required":["observations"]}],"properties":{"observations":{"items":{"additionalProperties":false,"properties":{"time":{"type":"number"},"value":{"type":["number","string"]}},"required":["time","value"],"type":"object"},"maxItems":10001,"minItems":1,"type":"array"},"value":{"type":["number","string"]}},"type":"object"},"maxProperties":100,"type":"object"},"data_mapping":{"additionalProperties":false,"properties":{"amount":{"maxLength":128,"type":["string","null"]},"blq":{"maxLength":128,"type":["string","null"]},"compartment":{"maxLength":128,"type":["string","null"]},"covariates":{"additionalProperties":{"maxLength":128,"minLength":1,"type":"string"},"maxProperties":100,"type":"object"},"dataset_content_sha256":{"pattern":"^[a-f0-9]{64}$","type":["string","null"]},"dataset_version_id":{"maxLength":128,"type":["string","null"]},"dependent_value":{"maxLength":128,"type":["string","null"]},"dose_event_values":{"items":{"type":["string","integer"]},"maxItems":20,"type":"array"},"duplicate_policy":{"default":"reject","enum":["reject","replicate_column"],"type":"string"},"duration":{"maxLength":128,"type":["string","null"]},"event_id":{"maxLength":128,"type":["string","null"]},"lloq":{"maxLength":128,"type":["string","null"]},"mapping_id":{"maxLength":128,"type":["string","null"]},"mapping_version":{"default":1,"minimum":1,"type":"integer"},"missing_value_policy":{"default":"reject","enum":["reject","drop_observation","explicit"],"type":"string"},"observation":{"maxLength":128,"type":["string","null"]},"observation_contexts":{"additionalProperties":{"additionalProperties":false,"properties":{"analyte_id":{"maxLength":128,"minLength":1,"pattern":"^[A-Za-z0-9][A-Za-z0-9_.-]*$","title":"Analyte Id","type":"string"},"compartment":{"maxLength":128,"minLength":1,"pattern":"^[A-Za-z0-9][A-Za-z0-9_.-]*$","title":"Compartment","type":"string"},"molecular_form":{"enum":["total","free","bound","conjugated","intact"],"title":"Molecular Form","type":"string"}},"required":["analyte_id","molecular_form","compartment"],"title":"MeasuredAnalyteContext","type":"object"},"maxProperties":200,"type":"object"},"observation_event_values":{"items":{"type":["string","integer"]},"maxItems":20,"type":"array"},"observation_units":{"additionalProperties":{"maxLength":64,"minLength":1,"type":"string"},"maxProperties":200,"type":"object"},"occasion":{"maxLength":128,"type":["string","null"]},"rate":{"maxLength":128,"type":["string","null"]},"replicate":{"maxLength":128,"type":["string","null"]},"role":{"maxLength":128,"minLength":1,"type":["string","null"]},"subject":{"maxLength":128,"type":["string","null"]},"time":{"default":"time","maxLength":128,"minLength":1,"type":"string"},"units":{"additionalProperties":{"maxLength":64,"minLength":1,"type":"string"},"maxProperties":200,"type":"object"}},"required":["mapping_version","time","missing_value_policy","duplicate_policy"],"type":"object"},"dosing_regimen":{"additionalProperties":false,"properties":{"doses":{"items":{"additionalProperties":false,"properties":{"amount":{"type":"number"},"duration":{"minimum":0,"type":"number"},"target":{"maxLength":128,"minLength":1,"type":"string"},"time":{"minimum":0,"type":"number"},"type":{"enum":["bolus","infusion"],"type":"string"}},"required":["time","amount","type","duration","target"],"type":"object"},"maxItems":100,"type":"array"}},"required":["doses"],"type":"object"},"initial_states":{"additionalProperties":{"type":"number"},"maxProperties":500,"type":"object"},"model_version_id":{"maxLength":128,"minLength":1,"type":"string"},"nlme_options":{"additionalProperties":false,"properties":{"compute_uncertainty":{"type":"boolean"},"inner_max_iterations":{"maximum":80,"minimum":1,"type":"integer"},"method":{"const":"focei","type":"string"},"random_seed":{"type":"integer"},"return_individual_predictions":{"type":"boolean"}},"required":["method","inner_max_iterations","compute_uncertainty","return_individual_predictions"],"type":"object"},"observable_column":{"const":"observable","type":"string"},"observed_data":{"items":{"additionalProperties":false,"properties":{"observable":{"maxLength":128,"minLength":1,"type":"string"},"role":{"enum":["calibration","validation","context"],"type":"string"},"subject_id":{"type":["string","number"]},"time":{"minimum":0,"type":"number"},"value":{"type":"number"}},"required":["time","observable","value"],"type":"object"},"maxItems":500,"minItems":2,"type":"array"},"optimizer_options":{"additionalProperties":false,"properties":{"abstol":{"exclusiveMinimum":0,"type":"number"},"compute_uncertainty":{"type":"boolean"},"max_iterations":{"maximum":80,"minimum":1,"type":"integer"},"reltol":{"exclusiveMinimum":0,"type":"number"}},"type":"object"},"parameters":{"additionalProperties":{"type":"number"},"maxProperties":2000,"type":"object"},"parameters_to_fit":{"additionalProperties":{"additionalProperties":false,"properties":{"bounds":{"items":{"type":"number"},"maxItems":2,"minItems":2,"type":"array"},"initial":{"type":"number"}},"required":["initial","bounds"],"type":"object"},"maxProperties":8,"minProperties":1,"propertyNames":{"pattern":"^[A-Za-z][A-Za-z0-9_]{0,127}$"},"type":"object"},"solver_options":{"additionalProperties":false,"properties":{"abstol":{"exclusiveMinimum":0,"type":"number"},"maxiters":{"minimum":1,"type":"integer"},"method":{"maxLength":64,"minLength":1,"type":"string"},"reltol":{"exclusiveMinimum":0,"type":"number"}},"type":"object"},"subject_id_column":{"const":"subject_id","type":"string"},"time_column":{"const":"time","type":"string"},"time_span":{"additionalProperties":false,"properties":{"end":{"type":"number"},"start":{"type":"number"},"step":{"exclusiveMinimum":0,"type":"number"}},"required":["start","end","step"],"type":"object"},"value_column":{"const":"value","type":"string"}},"required":["model_version_id","parameters_to_fit","backend","initial_states","parameters","dosing_regimen","time_span","time_column","observable_column","value_column","observed_data"],"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"pkpd.optimize_regimen","description":"Optimize fixed-time infusion amplitudes against an immutable model objective using automatic differentiation. Benchmark units; not clinical dose selection.","example":{"bindings":[],"capability_id":"pkpd.optimize_regimen","parameters":{"contract_id":"<contract_id>","max_iterations":40,"model_id":"<model_id>","model_version":"<model_version>","scenario_id":"<scenario_id>"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_controls":20,"max_dose_events":100,"max_iterations":80,"max_objective_samples":2001},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Optimize bounded dose amplitudes","outputs":[{"content_schema":null,"dataset_kind":null,"description":"Bounded amplitudes, objective improvement, convergence status, target trajectory and complete execution provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Dose optimization result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"contract_id":{"maxLength":128,"minLength":1,"title":"Optimization question","type":"string"},"initial_controls":{"default":null,"items":{"type":"number"},"maxItems":20,"minItems":1,"title":"Starting amplitudes","type":["array","null"]},"max_iterations":{"default":40,"maximum":80,"minimum":1,"title":"Iteration budget","type":"integer"},"model_id":{"maxLength":128,"minLength":1,"title":"Model","type":"string"},"model_version":{"maxLength":128,"minLength":1,"title":"Released model version","type":"string"},"scenario_id":{"maxLength":128,"minLength":1,"title":"Starting configuration","type":"string"}},"required":["model_id","scenario_id","contract_id","model_version"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"pkpd.parameter_scan","description":"Run a bounded one- or two-axis scan against a released or private immutable PK/PD or QSP model version and return the scientific response surface as one durable native job.","example":{"bindings":[],"capability_id":"pkpd.parameter_scan","parameters":{"covariates":{},"model_id":"<model_id>","scan_axes":[]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_output_columns":497,"max_output_rows_per_run":100000,"max_published_rows":100000,"max_scan_axes":2,"max_total_runs":25,"min_scan_axes":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Scan PK/PD model parameters","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The complete scan axes, bounded child simulations, comparison arrays, per-run status, and immutable execution provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Parameter comparison result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"base_dosing_regimen":{"default":null,"description":"Optional native dosing-regimen object.","title":"Baseline intervention","type":["object","null"]},"base_parameters":{"additionalProperties":{"type":"number"},"default":null,"title":"Baseline parameter adjustments","type":["object","null"]},"base_scenario_id":{"default":null,"description":"Optional released scientific scenario used as the scan baseline.","title":"Starting configuration","type":["string","null"]},"covariates":{"additionalProperties":{"additionalProperties":false,"anyOf":[{"required":["value"]},{"required":["observations"]}],"properties":{"observations":{"items":{"additionalProperties":false,"properties":{"time":{"type":"number"},"value":{"type":["number","string"]}},"required":["time","value"],"type":"object"},"minItems":1,"type":"array"},"value":{"type":["number","string"]}},"type":"object"},"default":{},"description":"Constant or time-varying covariate inputs applied to every scan run.","title":"Covariates","type":"object"},"initial_states":{"additionalProperties":{"type":"number"},"default":null,"title":"Initial-state adjustments","type":["object","null"]},"model_id":{"description":"PK/PD or QSP model identifier.","maxLength":200,"minLength":1,"title":"Model ID","type":"string"},"model_version":{"default":null,"description":"Optional immutable semantic model-package version.","title":"Model version","type":["string","null"]},"model_version_id":{"default":null,"description":"Optional private immutable library model version. The platform resolves its authoritative definition and typed IR server-side.","maxLength":128,"minLength":1,"title":"Private model version","type":["string","null"]},"scan_axes":{"description":"Exactly one or two mechanistic or dosing axes; their Cartesian product may contain at most 25 runs.","items":{"additionalProperties":false,"properties":{"key":{"minLength":1,"title":"Model quantity","type":"string"},"label":{"default":"","title":"Scientific label","type":"string"},"selector":{"default":null,"description":"Optional native selector for a documented dosing axis.","title":"Dosing-event selector","type":["object","null"]},"values":{"items":{"type":"number"},"maxItems":25,"minItems":1,"title":"Values to test","type":"array","uniqueItems":true}},"required":["key","values"],"type":"object"},"maxItems":2,"minItems":1,"title":"Scientific scan axes","type":"array"},"solver_options":{"default":null,"description":"Optional native solver method and tolerance object.","title":"Solver options","type":["object","null"]},"time_span":{"default":null,"description":"Optional native time-span object.","title":"Observation window","type":["object","null"]}},"required":["model_id","scan_axes"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"pkpd.scientific_analysis","description":"Run bounded simulation, estimation, diagnostics, sensitivity, uncertainty, optimization, and reporting analyses against one immutable private PK/PD or QSP model version.","example":{"bindings":[],"capability_id":"pkpd.scientific_analysis","parameters":{"analysis_type":"<analysis_type>","configuration":{}},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":[],"description":"Optional completed private-model fit for saved-fit residual diagnostics.","granularity":[],"max_items":1,"media_types":["application/json"],"min_items":0,"ordered":false,"required":false,"required_fields":[],"resource_kinds":["artifact"],"role":"fit_result","title":"Saved deterministic fit"},{"dataset_kinds":[],"description":"Completed private-model simulation for prediction comparison.","granularity":[],"max_items":1,"media_types":["application/json"],"min_items":0,"ordered":false,"required":false,"required_fields":[],"resource_kinds":["artifact"],"role":"simulation_a","title":"Simulation A"},{"dataset_kinds":[],"description":"Completed private-model simulation for prediction comparison.","granularity":[],"max_items":1,"media_types":["application/json"],"min_items":0,"ordered":false,"required":false,"required_fields":[],"resource_kinds":["artifact"],"role":"simulation_b","title":"Simulation B"},{"dataset_kinds":[],"description":"Completed deterministic fit for same-model residual comparison.","granularity":[],"max_items":1,"media_types":["application/json"],"min_items":0,"ordered":false,"required":false,"required_fields":[],"resource_kinds":["artifact"],"role":"fit_a","title":"Fit A"},{"dataset_kinds":[],"description":"Completed deterministic fit for same-model residual comparison.","granularity":[],"max_items":1,"media_types":["application/json"],"min_items":0,"ordered":false,"required":false,"required_fields":[],"resource_kinds":["artifact"],"role":"fit_b","title":"Fit B"}],"limits":{"max_analysis_parameters":20,"max_bayesian_chains":8,"max_bayesian_draws_per_chain":500,"max_configuration_bytes":5000000,"max_global_samples":8192,"max_metrics":30,"max_published_rows":1,"max_uncertainty_samples":200},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Analyze a private PK/PD model","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The complete sensitivity, identifiability, or uncertainty result, summary values, configuration, and immutable execution provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Model analysis result"}],"parameters_schema":{"$defs":{"EmpiricalPopulation":{"additionalProperties":false,"properties":{"assumptions":{"maxLength":1000,"minLength":1,"title":"Assumptions","type":"string"},"covariate_columns":{"additionalProperties":{"type":"string"},"maxProperties":50,"title":"Covariate Columns","type":"object"},"parameter_columns":{"additionalProperties":{"type":"string"},"maxProperties":50,"title":"Parameter Columns","type":"object"},"random_effect_columns":{"additionalProperties":{"type":"string"},"maxProperties":50,"title":"Random Effect Columns","type":"object"},"rows":{"items":{"additionalProperties":{"type":"number"},"type":"object"},"maxItems":10000,"minItems":2,"title":"Rows","type":"array"},"weights":{"items":{"type":"number"},"maxItems":10000,"minItems":2,"title":"Weights","type":"array"}},"required":["rows","weights","assumptions"],"title":"EmpiricalPopulation","type":"object"},"EndpointErrorBudget":{"additionalProperties":false,"properties":{"absolute":{"minimum":0,"title":"Absolute","type":"number"},"relative":{"maximum":1,"minimum":0,"title":"Relative","type":"number"}},"required":["absolute","relative"],"title":"EndpointErrorBudget","type":"object"},"SurrogateDecision":{"additionalProperties":false,"properties":{"direction":{"enum":["at_least","at_most"],"title":"Direction","type":"string"},"metric":{"maxLength":256,"minLength":1,"title":"Metric","type":"string"},"rationale":{"maxLength":1000,"minLength":1,"title":"Rationale","type":"string"},"threshold":{"title":"Threshold","type":"number"}},"required":["metric","threshold","direction","rationale"],"title":"SurrogateDecision","type":"object"},"bounds":{"additionalProperties":{"items":{"type":"number"},"maxItems":2,"minItems":2,"type":"array"},"maxProperties":20,"minProperties":1,"propertyNames":{"pattern":"^[A-Za-z][A-Za-z0-9_]{0,127}$"},"type":"object"},"commonProperties":{"action":{"enum":["train","evaluate"]},"artifact":{"maxProperties":5,"properties":{"design":{"$ref":"#/$defs/commonProperties/design"}},"required":["schema","binding","design","fit","reference"],"type":"object"},"bounds":{"$ref":"#/$defs/bounds"},"chains":{"maximum":8,"minimum":2,"type":"integer"},"confidence":{"exclusiveMaximum":1,"exclusiveMinimum":0,"type":"number"},"correlation":{"items":{"items":{"type":"number"},"maxItems":150,"minItems":1,"type":"array"},"maxItems":150,"minItems":1,"type":"array"},"covariate_distributions":{"$ref":"#/$defs/commonProperties/parameter_distributions"},"covariates":{"additionalProperties":{"additionalProperties":false,"oneOf":[{"required":["value"]},{"required":["observations"]}],"properties":{"observations":{"items":{"additionalProperties":false,"properties":{"time":{"type":"number"},"value":{"type":["number","string"]}},"required":["time","value"],"type":"object"},"maxItems":10001,"minItems":1,"type":"array"},"value":{"type":["number","string"]}},"type":"object"},"maxProperties":100,"type":"object"},"data_mapping":{"additionalProperties":{"maxLength":128,"minLength":1,"type":"string"},"maxProperties":100,"type":"object"},"design":{"additionalProperties":false,"properties":{"decision":{"anyOf":[{"$ref":"#/$defs/SurrogateDecision"},{"type":"null"}],"default":null},"degree":{"default":3,"maximum":3,"minimum":1,"title":"Degree","type":"integer"},"domain":{"additionalProperties":{"items":{"type":"number"},"type":"array"},"maxProperties":3,"minProperties":1,"title":"Domain","type":"object"},"error_budgets":{"additionalProperties":{"$ref":"#/$defs/EndpointErrorBudget"},"maxProperties":30,"minProperties":1,"title":"Error Budgets","type":"object"},"expected_reuse":{"items":{"type":"integer"},"maxItems":10,"minItems":1,"title":"Expected Reuse","type":"array"},"purpose":{"maxLength":1000,"minLength":1,"title":"Purpose","type":"string"},"response_transform":{"default":"log","enum":["identity","log"],"title":"Response Transform","type":"string"},"training_seed":{"default":410501,"maximum":4294967295,"minimum":0,"title":"Training Seed","type":"integer"},"training_size":{"default":64,"maximum":512,"minimum":16,"title":"Training Size","type":"integer"},"validation_seed":{"default":810503,"maximum":4294967295,"minimum":0,"title":"Validation Seed","type":"integer"},"validation_size":{"default":32,"maximum":256,"minimum":8,"title":"Validation Size","type":"integer"}},"required":["purpose","domain","error_budgets"],"title":"EndpointSurrogateDesign","type":"object"},"dose_decision":{"additionalProperties":false,"description":"Compare 2–6 dose multiples on the same virtual subjects. Population variation only; no numerical-tolerance or fitted-parameter uncertainty. The complete analysis is limited to 800 simulations.","properties":{"alternatives":{"items":{"additionalProperties":false,"properties":{"dose_multiplier":{"maximum":10,"minimum":0,"type":"number"},"id":{"maxLength":80,"minLength":1,"pattern":"^[A-Za-z0-9][A-Za-z0-9_.-]*$","type":"string"}},"required":["id","dose_multiplier"],"type":"object"},"maxItems":6,"minItems":2,"type":"array"},"assumptions":{"maxLength":2000,"minLength":1,"pattern":"\\S","type":"string"},"direction":{"default":"maximize","enum":["maximize","minimize"],"type":"string"},"limit":{"additionalProperties":false,"properties":{"operator":{"default":"le","enum":["le","ge"],"type":"string"},"summary":{"default":"cmax","enum":["final","auc","cmax","cmin","tmax"],"type":"string"},"value":{"type":"number"}},"required":["value"],"type":["object","null"]},"objective_summary":{"default":"auc","enum":["final","auc","cmax","cmin","tmax"],"type":"string"},"observable":{"maxLength":128,"minLength":1,"type":"string"},"tie_tolerance":{"default":1e-09,"minimum":0,"type":"number"}},"required":["alternatives","observable","assumptions"],"type":["object","null"]},"dosing_regimen":{"additionalProperties":false,"properties":{"doses":{"items":{"additionalProperties":false,"properties":{"amount":{"type":"number"},"duration":{"minimum":0,"type":"number"},"target":{"maxLength":128,"minLength":1,"type":"string"},"time":{"minimum":0,"type":"number"},"type":{"enum":["bolus","infusion"],"type":"string"}},"required":["time","amount","type","duration","target"],"type":"object"},"maxItems":100,"type":"array"}},"required":["doses"],"type":"object"},"draws":{"maximum":500,"minimum":20,"type":"integer"},"evaluation_points":{"items":{"additionalProperties":false,"properties":{"final_confirmation":{"default":true,"title":"Final Confirmation","type":"boolean"},"id":{"maxLength":128,"minLength":1,"title":"Id","type":"string"},"parameters":{"additionalProperties":{"type":"number"},"maxProperties":3,"minProperties":1,"title":"Parameters","type":"object"},"uncertainty_critical":{"default":false,"title":"Uncertainty Critical","type":"boolean"}},"required":["id","parameters"],"title":"SurrogateEvaluationPoint","type":"object"},"maxItems":100,"minItems":1,"type":"array"},"exact_budget":{"maximum":100,"minimum":0,"type":"integer"},"initial_states":{"additionalProperties":{"type":"number"},"maxProperties":500,"type":"object"},"levels":{"maximum":100,"minimum":4,"type":"integer"},"method":{"enum":["auto","forward","adjoint","finite_difference","latin_hypercube","random","sobol","morris","correlated_rank"],"type":"string"},"metrics":{"items":{"additionalProperties":false,"properties":{"label":{"maxLength":128,"minLength":1,"type":"string"},"observable":{"pattern":"^[A-Za-z][A-Za-z0-9_]{0,127}$","type":"string"},"summary":{"enum":["final","auc","cmax","cmin","tmax"],"type":"string"}},"required":["observable","summary"],"type":"object"},"maxItems":30,"minItems":1,"type":"array"},"model_version_id":{"maxLength":128,"minLength":1,"type":"string"},"n":{"maximum":8192,"minimum":2,"type":"integer"},"observables":{"items":{"pattern":"^[A-Za-z][A-Za-z0-9_]{0,127}$","type":"string"},"maxItems":20,"minItems":1,"type":"array","uniqueItems":true},"observation_sd":{"exclusiveMinimum":0,"type":"number"},"observation_sd_by_observable":{"additionalProperties":{"exclusiveMinimum":0,"type":"number"},"maxProperties":20,"type":"object"},"observation_times":{"items":{"type":"number"},"maxItems":2000,"minItems":1,"type":"array","uniqueItems":true},"observations":{"items":{"additionalProperties":false,"properties":{"observable":{"maxLength":128,"minLength":1,"type":"string"},"standard_deviation":{"exclusiveMinimum":0,"type":"number"},"time":{"type":"number"},"value":{"type":"number"}},"required":["observable","time","value","standard_deviation"],"type":"object"},"maxItems":5000,"minItems":2,"type":"array"},"parameter_distributions":{"additionalProperties":{"additionalProperties":true,"properties":{"distribution":{"enum":["fixed","categorical","uniform","loguniform","normal","truncated_normal","lognormal"],"type":"string"},"lower":{"type":"number"},"upper":{"type":"number"}},"required":["distribution"],"type":"object"},"maxProperties":50,"minProperties":1,"type":"object"},"parameter_proposal_scales":{"additionalProperties":{"exclusiveMinimum":0,"type":"number"},"maxProperties":20,"minProperties":1,"type":"object"},"parameter_scales":{"additionalProperties":{"exclusiveMinimum":0,"type":"number"},"maxProperties":20,"type":"object"},"parameters":{"additionalProperties":{"type":"number"},"maxProperties":2000,"type":"object"},"parameters_to_analyze":{"items":{"pattern":"^[A-Za-z][A-Za-z0-9_]{0,127}$","type":"string"},"maxItems":20,"minItems":1,"type":"array","uniqueItems":true},"payload":{"maxProperties":500,"type":"object"},"posterior_predictive_draws":{"maximum":50,"minimum":0,"type":"integer"},"previous_states":{"maxProperties":8,"type":"object"},"quantiles":{"items":{"exclusiveMaximum":1,"exclusiveMinimum":0,"type":"number"},"maxItems":9,"minItems":1,"type":"array"},"random_effect_distributions":{"$ref":"#/$defs/commonProperties/parameter_distributions"},"relative_rank_tolerance":{"maximum":0.1,"minimum":1e-12,"type":"number"},"seed":{"maximum":2147483647,"minimum":1,"type":"integer"},"solver_options":{"additionalProperties":false,"properties":{"abstol":{"exclusiveMinimum":0,"type":"number"},"maxiters":{"minimum":1,"type":"integer"},"method":{"maxLength":64,"minLength":1,"type":"string"},"reltol":{"exclusiveMinimum":0,"type":"number"}},"type":"object"},"time_span":{"additionalProperties":false,"properties":{"end":{"type":"number"},"start":{"type":"number"},"step":{"exclusiveMinimum":0,"type":"number"}},"required":["start","end","step"],"type":"object"},"trajectories":{"maximum":1000,"minimum":4,"type":"integer"}}},"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"allOf":[{"if":{"properties":{"analysis_type":{"const":"local_sensitivity"}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"required":["model_version_id","parameters_to_analyze","metrics","method"]}}}},{"if":{"properties":{"analysis_type":{"const":"identifiability"}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"required":["model_version_id","parameters_to_analyze","observables","observation_sd"]}}}},{"if":{"properties":{"analysis_type":{"const":"uncertainty"}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"required":["model_version_id","parameter_distributions","metrics","n","seed","method","quantiles"]}}}},{"if":{"properties":{"analysis_type":{"const":"global_sensitivity"}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"oneOf":[{"required":["bounds"]},{"required":["parameter_distributions"]}],"required":["model_version_id","metrics","method","n","seed"]}}}},{"if":{"properties":{"analysis_type":{"const":"population_simulation"}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"anyOf":[{"required":["parameter_distributions"]},{"required":["random_effect_distributions"]},{"required":["covariate_distributions"]},{"required":["empirical_population"]}],"required":["model_version_id","observables","n","seed","method","quantiles"]}}}},{"if":{"properties":{"analysis_type":{"const":"bayesian_estimation"}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"required":["model_version_id","parameter_proposal_scales","observations","chains","draws","seed","posterior_predictive_draws","confidence"]}}}},{"if":{"properties":{"analysis_type":{"enum":["fit_diagnostics","parameter_uncertainty","model_comparison","profile_likelihood","virtual_population_calibration","candidate_selection","adc_composition","system_translation","mcmc_diagnostics","covariate_selection","trial_design","nca","report"]}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"required":["model_version_id","payload"]}}}},{"if":{"properties":{"analysis_type":{"const":"surrogate"}},"required":["analysis_type"]},"then":{"properties":{"configuration":{"allOf":[{"else":{"required":["artifact","evaluation_points","exact_budget"]},"if":{"properties":{"action":{"const":"train"}}},"then":{"required":["design"]}}],"properties":{"metrics":{"items":{"properties":{"summary":{"enum":["final","auc","cmax"]}}}}},"required":["model_version_id","action","metrics"]}}}},{"if":{"properties":{"configuration":{"required":["dose_decision"]}}},"then":{"properties":{"analysis_type":{"const":"population_simulation"}}}},{"if":{"properties":{"configuration":{"required":["empirical_population"]}}},"then":{"properties":{"analysis_type":{"const":"population_simulation"},"configuration":{"not":{"anyOf":[{"required":["parameter_distributions"]},{"required":["random_effect_distributions"]},{"required":["covariate_distributions"]},{"required":["correlation"]}]},"properties":{"method":{"const":"random"}}}}}}],"properties":{"analysis_type":{"enum":["local_sensitivity","identifiability","uncertainty","population_simulation","bayesian_estimation","global_sensitivity","fit_diagnostics","parameter_uncertainty","model_comparison","profile_likelihood","virtual_population_calibration","candidate_selection","adc_composition","system_translation","mcmc_diagnostics","covariate_selection","trial_design","nca","report","surrogate"],"type":"string"},"configuration":{"additionalProperties":false,"properties":{"action":{"$ref":"#/$defs/commonProperties/action"},"artifact":{"$ref":"#/$defs/commonProperties/artifact"},"bounds":{"$ref":"#/$defs/commonProperties/bounds"},"chains":{"$ref":"#/$defs/commonProperties/chains"},"confidence":{"$ref":"#/$defs/commonProperties/confidence"},"correlation":{"$ref":"#/$defs/commonProperties/correlation"},"covariate_distributions":{"$ref":"#/$defs/commonProperties/covariate_distributions"},"covariates":{"$ref":"#/$defs/commonProperties/covariates"},"data_mapping":{"$ref":"#/$defs/commonProperties/data_mapping"},"design":{"$ref":"#/$defs/commonProperties/design"},"dose_decision":{"$ref":"#/$defs/commonProperties/dose_decision"},"dosing_regimen":{"$ref":"#/$defs/commonProperties/dosing_regimen"},"draws":{"$ref":"#/$defs/commonProperties/draws"},"empirical_population":{"$ref":"#/$defs/EmpiricalPopulation"},"evaluation_points":{"$ref":"#/$defs/commonProperties/evaluation_points"},"exact_budget":{"$ref":"#/$defs/commonProperties/exact_budget"},"initial_states":{"$ref":"#/$defs/commonProperties/initial_states"},"levels":{"$ref":"#/$defs/commonProperties/levels"},"method":{"$ref":"#/$defs/commonProperties/method"},"metrics":{"$ref":"#/$defs/commonProperties/metrics"},"model_version_id":{"$ref":"#/$defs/commonProperties/model_version_id"},"n":{"$ref":"#/$defs/commonProperties/n"},"observables":{"$ref":"#/$defs/commonProperties/observables"},"observation_sd":{"$ref":"#/$defs/commonProperties/observation_sd"},"observation_sd_by_observable":{"$ref":"#/$defs/commonProperties/observation_sd_by_observable"},"observation_times":{"$ref":"#/$defs/commonProperties/observation_times"},"observations":{"$ref":"#/$defs/commonProperties/observations"},"parameter_distributions":{"$ref":"#/$defs/commonProperties/parameter_distributions"},"parameter_proposal_scales":{"$ref":"#/$defs/commonProperties/parameter_proposal_scales"},"parameter_scales":{"$ref":"#/$defs/commonProperties/parameter_scales"},"parameters":{"$ref":"#/$defs/commonProperties/parameters"},"parameters_to_analyze":{"$ref":"#/$defs/commonProperties/parameters_to_analyze"},"payload":{"$ref":"#/$defs/commonProperties/payload"},"posterior_predictive_draws":{"$ref":"#/$defs/commonProperties/posterior_predictive_draws"},"previous_states":{"$ref":"#/$defs/commonProperties/previous_states"},"quantiles":{"$ref":"#/$defs/commonProperties/quantiles"},"random_effect_distributions":{"$ref":"#/$defs/commonProperties/random_effect_distributions"},"relative_rank_tolerance":{"$ref":"#/$defs/commonProperties/relative_rank_tolerance"},"seed":{"$ref":"#/$defs/commonProperties/seed"},"solver_options":{"$ref":"#/$defs/commonProperties/solver_options"},"time_span":{"$ref":"#/$defs/commonProperties/time_span"},"trajectories":{"$ref":"#/$defs/commonProperties/trajectories"}},"type":"object"}},"required":["analysis_type","configuration"],"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.2.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"pkpd.simulate_scenario","description":"Run a named, version-pinned PK/PD or QSP model scenario with optional parameter, state, dosing, time-span, and solver overrides.","example":{"bindings":[],"capability_id":"pkpd.simulate_scenario","parameters":{"model_id":"<model_id>","scenario_id":"<scenario_id>"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_output_columns":2000,"max_output_rows":1000000,"max_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Simulate a PK/PD scenario","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The complete time grid and output arrays with model, scenario, runtime, solver, integrity, and immutable execution provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Simulation result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"dosing_override":{"default":null,"description":"Optional native dosing-regimen JSON object.","title":"Dosing override","type":["object","null"]},"initial_state_overrides":{"additionalProperties":{"type":"number"},"default":null,"description":"Optional numeric initial-state overrides as a JSON object.","title":"Initial-state overrides","type":["object","null"]},"model_id":{"description":"Released PK/PD or QSP model identifier.","maxLength":200,"minLength":1,"title":"Model ID","type":"string"},"model_version":{"default":null,"description":"Optional immutable semantic model-package version.","title":"Model version","type":["string","null"]},"parameter_overrides":{"additionalProperties":{"type":"number"},"default":null,"description":"Optional numeric parameter overrides as a JSON object.","title":"Parameter overrides","type":["object","null"]},"scenario_id":{"description":"Named scenario preset identifier.","maxLength":200,"minLength":1,"title":"Scenario ID","type":"string"},"solver_options":{"default":null,"description":"Optional native solver method and tolerance JSON object.","title":"Solver options","type":["object","null"]},"time_span_override":{"default":null,"description":"Optional native time-span JSON object.","title":"Time-span override","type":["object","null"]}},"required":["model_id","scenario_id"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"2.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"pkpd.simulate_user_model","description":"Simulate an immutable, validated user-owned PK/PD or QSP model definition with explicit states, parameters, dosing, time span, and solver controls.","example":{"bindings":[],"capability_id":"pkpd.simulate_user_model","parameters":{"dosing_regimen":{"doses":[]},"initial_states":{},"model_version_id":"<model_version_id>","parameters":{},"time_span":{"end":1.0,"start":1.0,"step":1.0}},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_output_columns":2000,"max_output_rows":1000000,"max_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Simulate a private PK/PD model","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The complete private-model time grid, output arrays with declared units, solver record, and immutable execution provenance.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Simulation result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"covariates":{"additionalProperties":{"additionalProperties":false,"oneOf":[{"required":["value"]},{"required":["observations"]}],"properties":{"observations":{"items":{"additionalProperties":false,"properties":{"time":{"type":"number"},"value":{"type":["number","string"]}},"required":["time","value"],"type":"object"},"maxItems":10001,"minItems":1,"type":"array"},"value":{"type":["number","string"]}},"type":"object"},"maxProperties":100,"type":"object"},"dosing_regimen":{"additionalProperties":false,"properties":{"doses":{"items":{"additionalProperties":false,"properties":{"amount":{"type":"number"},"duration":{"minimum":0,"type":"number"},"target":{"maxLength":128,"minLength":1,"type":"string"},"time":{"minimum":0,"type":"number"},"type":{"enum":["bolus","infusion"],"type":"string"}},"required":["time","amount","type","duration","target"],"type":"object"},"maxItems":100,"type":"array"}},"required":["doses"],"type":"object"},"initial_states":{"additionalProperties":{"type":"number"},"maxProperties":500,"type":"object"},"model_version_id":{"maxLength":128,"minLength":1,"type":"string"},"parameters":{"additionalProperties":{"type":"number"},"maxProperties":2000,"type":"object"},"solver_options":{"additionalProperties":false,"default":null,"properties":{"abstol":{"exclusiveMinimum":0,"type":"number"},"maxiters":{"minimum":1,"type":"integer"},"method":{"maxLength":64,"minLength":1,"type":"string"},"reltol":{"exclusiveMinimum":0,"type":"number"}},"type":["object","null"]},"time_span":{"additionalProperties":false,"properties":{"end":{"type":"number"},"start":{"type":"number"},"step":{"exclusiveMinimum":0,"type":"number"}},"required":["start","end","step"],"type":"object"}},"required":["model_version_id","initial_states","parameters","dosing_regimen","time_span"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"pkpd","version":null},{"display_name":"Proteina-Complexa","license":"Apache-2.0 for source; separate checkpoint and bundled-component terms","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"proteina_complexa.design_ligand_binders","description":"Generate de novo protein sequence/backbone candidates around one checksum-bound posed small molecule with NVIDIA Proteina-Complexa v1.1.0. RF3/AF2 reward search and AME motif scaffolding are not part of this operation.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"ligand_residue_name":"<value>","ligand_structure_artifact_id":"<value>","ligand_structure_checksum_sha256":"<value>","smiles":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"ligands"}],"capability_id":"proteina_complexa.design_ligand_binders","parameters":{"mode":"ligand_binder","num_designs":1,"protein_length":120,"seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures","table"],"description":"One ligand-only PDB pose plus SMILES in matching atom order and exact immutable Artifact evidence.","granularity":["selection","dataset_version"],"max_items":1,"media_types":["chemical/x-pdb"],"min_items":1,"ordered":true,"required":true,"required_fields":["ligand_structure_artifact_id","ligand_structure_checksum_sha256","ligand_residue_name","smiles"],"resource_kinds":["inline"],"role":"ligands","title":"Posed ligand and chemical identity"}],"limits":{"max_designs_per_job":4,"max_ligand_atoms":256,"max_ligand_bytes":2097152,"max_rows_per_job":1,"max_sequence_length":256,"max_smiles_bytes":4096,"min_rows_per_job":1,"min_sequence_length":40},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design ligand binders with Proteina-Complexa","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable Dataset of generated binder complexes retaining the exact posed ligand, chemical identity evidence, sequences, and checksum-bound structure Artifacts. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"generated_structures","title":"Posed-ligand binder candidates"},{"content_schema":null,"dataset_kind":null,"description":"The immutable validated native result, request digest, runtime identity, and artifact inventory.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Proteina-Complexa result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"mode":{"const":"ligand_binder","default":"ligand_binder","description":"Pinned posed-ligand binder generation mode.","title":"Mode","type":"string"},"num_designs":{"default":1,"description":"Number of sequence/backbone and ligand-complex pairs generated.","maximum":4,"minimum":1,"title":"Designs","type":"integer"},"protein_length":{"default":120,"description":"Generated protein length in residues.","maximum":256,"minimum":40,"title":"Protein length","type":"integer"},"seed":{"default":0,"description":"Non-negative deterministic sampling seed.","maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"}},"type":"object"},"resource_class":"gpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/NVIDIA-BioNeMo/Proteina-Complexa","tool_id":"proteina-complexa","version":"1.0.0 pinned source profile"},{"display_name":"ProteinMPNN","license":"MIT; released model assets CC-BY-4.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":2,"max_rows_per_native_batch":2,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"ligandmpnn.design_ligand_conditioned_sequences","description":"Generate protein sequence candidates conditioned on checksum-bound full-backbone PDB structures and their non-water atomic context, including small molecules, nucleic acids, metals, and other non-protein atoms.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"ligandmpnn.design_ligand_conditioned_sequences","parameters":{"fixed_positions":{},"ligand_score_cutoff_angstrom":8.0,"model_name":"v_32_010_25","num_sequences":4,"omit_amino_acids":[],"sampling_temperature":0.1,"seed":42},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version containing checksum-bound full-backbone PDB Artifacts with at least one non-water atomic-context record.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Protein structures with atomic context"}],"limits":{"max_native_batch_size":2,"max_pdb_bytes_per_job":4194304,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":2,"max_sequences_per_structure":16,"max_total_residues":2000,"min_rows_per_job":1,"required_atomic_context":"at_least_one_non_water_non_protein_atom","supported_alphabet":"unambiguous_protein","supported_structure_media_type":"chemical/x-pdb"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design ligand-conditioned protein sequences with LigandMPNN","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable sample-expanded Dataset retaining source structure and atomic-context evidence, exact designed chain sequences, overall and ligand-context confidence, recovery, mutations, selected checkpoint, parameters, digests, row status, and lineage. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_sequences","title":"LigandMPNN sequence designs"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified LigandMPNN response containing full PDB, protein and atomic-context counts, chain, residue, sample, confidence, checkpoint, source, request, row, batch, and measured execution evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native LigandMPNN result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"design_chains":{"default":null,"description":"Ordered one-character PDB chain IDs to redesign. Null redesigns every protein chain.","items":{"pattern":"^[A-Za-z0-9]$","type":"string"},"maxItems":16,"minItems":1,"title":"Chains to design","type":["array","null"],"uniqueItems":true},"fixed_positions":{"additionalProperties":{"items":{"minimum":1,"type":"integer"},"minItems":1,"type":"array","uniqueItems":true},"default":{},"description":"Per-chain sorted unique one-based sequence positions that remain fixed during design.","propertyNames":{"pattern":"^[A-Za-z0-9]$"},"title":"Fixed sequence positions","type":"object"},"ligand_score_cutoff_angstrom":{"default":8.0,"description":"Atomic-context distance cutoff used for the reported ligand-aware score.","maximum":12.0,"minimum":4.0,"title":"Atomic-context score cutoff","type":"number"},"model_name":{"default":"v_32_010_25","description":"Select the official 32-neighbor, 25-atom-context checkpoint trained with 0.05, 0.10, 0.20, or 0.30 angstrom coordinate noise.","enum":["v_32_005_25","v_32_010_25","v_32_020_25","v_32_030_25"],"title":"Checkpoint training noise","type":"string"},"num_sequences":{"default":4,"maximum":16,"minimum":1,"title":"Sequences per structure","type":"integer"},"omit_amino_acids":{"default":[],"description":"Sorted unique canonical amino acids excluded from sampling.","items":{"enum":["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"],"type":"string"},"maxItems":19,"title":"Omitted amino acids","type":"array","uniqueItems":true},"sampling_temperature":{"default":0.1,"maximum":1.0,"minimum":0.05,"title":"Sampling temperature","type":"number"},"seed":{"default":42,"description":"A positive base seed. Record i uses seed+i in stable input order.","maximum":2147483645,"minimum":1,"title":"Deterministic base seed","type":"integer"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":2,"max_rows_per_native_batch":2,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"proteinmpnn.design_protein_sequences","description":"Generate structure-conditioned protein sequence candidates from checksum-bound full-backbone PDB structures with explicit chain and fixed-position constraints, deterministic sampling, and a choice of all four official vanilla or all four official soluble-protein checkpoints.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"proteinmpnn.design_protein_sequences","parameters":{"backbone_noise_angstrom":0.0,"fixed_positions":{},"model_family":"vanilla","model_name":"v_48_020","num_sequences":4,"omit_amino_acids":[],"sampling_temperature":0.1,"seed":42},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version containing checksum-bound PDB Artifacts with complete N, CA, C, and O coordinates for every supported protein residue.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Protein structures"}],"limits":{"max_native_batch_size":2,"max_pdb_bytes_per_job":4194304,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":2,"max_sequences_per_structure":16,"max_total_residues":2000,"min_rows_per_job":1,"supported_alphabet":"unambiguous_protein","supported_structure_media_type":"chemical/x-pdb"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design protein sequences with ProteinMPNN","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable sample-expanded Dataset retaining source structure evidence, exact designed chain sequences, scores, recovery, mutations, selected model family/checkpoint/training noise, parameters, digests, row status, and lineage. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_sequences","title":"ProteinMPNN sequence designs"},{"content_schema":null,"dataset_kind":null,"description":"The immutable checksum-verified response containing full PDB, chain, residue, sample, score, selected vanilla or soluble checkpoint, source, request, row, and batch evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native ProteinMPNN result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"backbone_noise_angstrom":{"default":0.0,"maximum":1.0,"minimum":0.0,"title":"Backbone noise","type":"number"},"design_chains":{"default":null,"description":"Ordered one-character PDB chain IDs to redesign. Null redesigns every protein chain.","items":{"pattern":"^[A-Za-z0-9]$","type":"string"},"maxItems":16,"minItems":1,"title":"Chains to design","type":["array","null"],"uniqueItems":true},"fixed_positions":{"additionalProperties":{"items":{"minimum":1,"type":"integer"},"minItems":1,"type":"array","uniqueItems":true},"default":{},"description":"Per-chain sorted unique one-based sequence positions that remain fixed during design.","propertyNames":{"pattern":"^[A-Za-z0-9]$"},"title":"Fixed sequence positions","type":"object"},"model_family":{"default":"vanilla","description":"Use vanilla for general protein design or soluble for the soluble-protein-only training family.","enum":["vanilla","soluble"],"title":"Checkpoint family","type":"string"},"model_name":{"default":"v_48_020","description":"Select the official 48-neighbor checkpoint trained with 0.02, 0.10, 0.20, or 0.30 angstrom coordinate noise.","enum":["v_48_002","v_48_010","v_48_020","v_48_030"],"title":"Checkpoint training noise","type":"string"},"num_sequences":{"default":4,"maximum":16,"minimum":1,"title":"Sequences per structure","type":"integer"},"omit_amino_acids":{"default":[],"description":"Sorted unique canonical amino acids excluded from sampling.","items":{"enum":["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"],"type":"string"},"maxItems":19,"title":"Omitted amino acids","type":"array","uniqueItems":true},"sampling_temperature":{"default":0.1,"maximum":1.0,"minimum":0.05,"title":"Sampling temperature","type":"number"},"seed":{"default":42,"description":"A positive base seed. Record i uses seed+i in stable input order.","maximum":2147483645,"minimum":1,"title":"Deterministic base seed","type":"integer"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.3.0"}],"source_repository":"https://github.com/dauparas/ProteinMPNN","tool_id":"proteinmpnn","version":"pinned 2026 release profile"},{"display_name":"Protenix-v2","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":8,"max_rows_per_native_batch":8,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"protenix.predict_complex_cohort","description":"Predict a bounded native cohort of target-binder complexes with Protenix-v2, explicit sampling seeds, deterministic fixed-seed execution, per-token PAE, confidence evidence, structured row failures, and checksum-bound artifact publication.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"binder_sequence":"<value>","target_sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"candidates"}],"capability_id":"protenix.predict_complex_cohort","parameters":{"binder_sequence_column":"binder_sequence","seeds":[0],"target_msa_artifact_column":"target_msa_artifact_id","target_sequence_column":"target_sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","structures","comparison"],"description":"One frozen Selection or immutable Dataset Version containing explicit target and binder sequences; rows may additionally bind a target A3M Artifact and a reference complex Artifact for downstream scoring.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["target_sequence","binder_sequence"],"resource_kinds":["inline"],"role":"candidates","title":"Target and binder sequence cohort"}],"limits":{"max_binder_length":500,"max_msa_bytes_per_row":16777216,"max_output_bytes_per_job":536870912,"max_rows_per_job":8,"max_rows_per_native_batch":8,"max_seeds":5,"max_structure_bytes_per_artifact":8388608,"max_target_length":2000,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict a binder complex cohort with Protenix-v2","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable seed-expanded Dataset with checksum-bound model structures and per-token PAE evidence, explicit row failures, and optional reference-complex bindings. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"predicted_complexes","title":"Predicted target-binder complexes"},{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified structure, PAE, or confidence Artifact published by the exact released image.","media_type":null,"resource_kind":"artifact","role":"predicted_artifact","title":"Protenix prediction Artifact"},{"content_schema":null,"dataset_kind":null,"description":"The immutable cohort response retaining release, sampling, runtime, model, per-row failure, Artifact, and digest evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Protenix result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"binder_sequence_column":{"default":"binder_sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Binder sequence column","type":"string"},"seeds":{"default":[0],"items":{"maximum":2147483647,"minimum":0,"type":"integer"},"maxItems":5,"minItems":1,"title":"Sampling seeds","type":"array","uniqueItems":true},"target_msa_artifact_column":{"default":"target_msa_artifact_id","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional target MSA Artifact column","type":"string"},"target_sequence_column":{"default":"target_sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Target sequence column","type":"string"}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/bytedance/Protenix","tool_id":"protenix","version":"2.0.0"},{"display_name":"PXDesign","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":4,"max_rows_per_native_batch":4,"mode":"native_batch","native_batch_unit":"groups","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"pxdesign.design_protein_binders","description":"Generate protein-target binder proposals with the pinned PXDesign source boundary in batches of up to four heterogeneous targets and four designs per target. This operation does not support lipid or small-molecule conditioning.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"binder_length":"<value>","item_id":"<value>","structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","target_chains":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"targets"}],"capability_id":"pxdesign.design_protein_binders","parameters":{"designs_per_item":1,"seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One to four immutable checksum-bound protein target structures. Each row declares a stable item ID, target chains, optional hotspots, and binder length.","granularity":["selection","dataset_version"],"max_items":4,"media_types":["chemical/x-pdb","chemical/x-mmcif"],"min_items":1,"ordered":true,"required":true,"required_fields":["item_id","structure_artifact_id","structure_checksum_sha256","target_chains","binder_length"],"resource_kinds":["inline"],"role":"targets","title":"Protein target structure"}],"limits":{"binder_length_max":200,"binder_length_min":31,"max_designs_per_item":4,"max_rows_per_job":4,"max_structure_bytes":8000000},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design protein-target binders with PXDesign","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable row-preserving Dataset for up to four targets and four generated binders per target, with checksum-bound structures and native metrics. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"binder_designs","title":"PXDesign binder candidates"},{"content_schema":null,"dataset_kind":null,"description":"A checksum-verified binder-target structure from the exact qualified PXDesign image.","media_type":"chemical/x-mmcif","resource_kind":"artifact","role":"designed_structure","title":"PXDesign structure"},{"content_schema":null,"dataset_kind":null,"description":"The immutable validated native batch result, execution metrics, and artifact inventory.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native PXDesign result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"designs_per_item":{"default":1,"description":"Number of binder structures generated for each selected target row.","maximum":4,"minimum":1,"title":"Designs per target","type":"integer"},"seed":{"default":0,"description":"Base deterministic sampling seed for the ordered target batch.","maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"}},"type":"object"},"resource_class":"gpu-large","side_effect_class":"expensive_compute","version":"0.2.0"}],"source_repository":"https://github.com/bytedance/PXDesign","tool_id":"pxdesign","version":"0.2.0 pinned batch profile"},{"display_name":"PyContact-MS","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"py_contact_ms.analyze_complex_contacts","description":"Compute checksum-bound contact molecular-surface (CMS) evidence for explicit binder and target PDB chains with the pinned py-contact-ms CPU implementation.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"py_contact_ms.analyze_complex_contacts","parameters":{"binder_chains":[],"include_binder_side":true,"include_max_possible":true,"target_chains":[]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"Immutable PDB structures with checksums and explicit binder/target chain groups.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256","structure_size_bytes","structure_media_type"],"resource_kinds":["inline"],"role":"structures","title":"Complex structures"}],"limits":{"max_pdb_bytes_per_job":8388608,"max_pdb_bytes_per_row":2097152,"max_rows_per_job":1,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Analyze complex contacts with py-contact-ms","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Row-preserving Structures dataset with target and binder CMS, normalized target CMS, atom counts, and reconstructable per-residue evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"contact_molecular_surface","title":"Contact molecular-surface analysis"},{"content_schema":null,"dataset_kind":null,"description":"Digest-bound native response with exact source revision, request/result digests, chain scope, and ordered partial-failure evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Pinned py-contact-ms native result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"binder_chains":{"items":{"pattern":"^[A-Za-z0-9]$","type":"string"},"maxItems":8,"minItems":1,"title":"Binder chains","type":"array","uniqueItems":true},"include_binder_side":{"default":true,"type":"boolean"},"include_max_possible":{"default":true,"type":"boolean"},"target_chains":{"items":{"pattern":"^[A-Za-z0-9]$","type":"string"},"maxItems":8,"minItems":1,"title":"Target chains","type":"array","uniqueItems":true}},"required":["binder_chains","target_chains"],"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"2.0.0"}],"source_repository":"https://github.com/ullahsamee/py_contact_ms","tool_id":"py-contact-ms","version":"algorithm 1.0.0"},{"display_name":"RFantibody","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"rfantibody.design_antibody_structures","description":"Run one bounded antibody cascade from immutable target and framework PDBs through RFdiffusion, ProteinMPNN, and RF2. Nanobody mode and multi-design sampling remain unreleased.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"targets"},{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"frameworks"}],"capability_id":"rfantibody.design_antibody_structures","parameters":{"design_loops":"<design_loops>","hotspot_residues":[],"mode":"antibody","seed":0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"Exact immutable input bound by the canonical Run.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256"],"resource_kinds":["inline"],"role":"targets","title":"Target structures"},{"dataset_kinds":["structures"],"description":"One immutable antibody framework PDB passed into the same released cascade.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256"],"resource_kinds":["inline"],"role":"frameworks","title":"Framework structure"}],"limits":{"max_designs_per_job":1,"max_pdb_bytes_per_input":2097152,"max_rows_per_job":1,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design an antibody structure with RFantibody","outputs":[{"content_schema":null,"dataset_kind":null,"description":"The immutable final RF2 structure from the same RFdiffusion and ProteinMPNN cascade.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"predicted_structure","title":"RFantibody RF2 final design"},{"content_schema":null,"dataset_kind":null,"description":"Validated stage checksums, model identities, CUDA evidence, and the exact final structure.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"RFantibody cascade result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"design_loops":{"maxLength":128,"minLength":6,"pattern":"^\\[(?:[HL][123]:(?:[0-9]{1,2}(?:-[0-9]{1,2})?))(?:,[HL][123]:(?:[0-9]{1,2}(?:-[0-9]{1,2})?))*\\]$","type":"string"},"hotspot_residues":{"items":{"pattern":"^[A-Za-z0-9][0-9]{1,5}$","type":"string"},"maxItems":8,"minItems":1,"type":"array","uniqueItems":true},"mode":{"const":"antibody","default":"antibody"},"seed":{"const":0,"default":0}},"required":["mode","hotspot_residues","design_loops"],"type":"object"},"resource_class":"gpu-small","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://github.com/RosettaCommons/RFantibody","tool_id":"rfantibody","version":"pinned antibody cascade release"},{"display_name":"RFdiffusion","license":"BSD-3-Clause","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"rfdiffusion.generate_unconditional_backbone","description":"Generate one deterministic 20–50-residue unconditional backbone with the pinned RFdiffusion Base checkpoint. Motif, binder, and symmetric modes remain unreleased.","example":{"bindings":[],"capability_id":"rfdiffusion.generate_unconditional_backbone","parameters":{"diffusion_steps":15,"length":20},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[],"limits":{"max_designs_per_job":1,"max_diffusion_steps":50,"max_length":50,"max_pdb_bytes_per_job":2097152,"max_rows_per_job":1,"min_diffusion_steps":15,"min_length":20},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Generate an unconditional protein backbone with RFdiffusion","outputs":[{"content_schema":null,"dataset_kind":null,"description":"An immutable PDB containing the one checksum-verified deterministic unconditional backbone produced by the pinned Base checkpoint.","media_type":"chemical/x-pdb","resource_kind":"artifact","role":"predicted_structure","title":"RFdiffusion unconditional backbone"},{"content_schema":null,"dataset_kind":null,"description":"The immutable native contract with checkpoint identity, bounded parameters, reconstructed structure evidence, and exact result digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native RFdiffusion unconditional result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"diffusion_steps":{"default":15,"maximum":50,"minimum":15,"type":"integer"},"length":{"default":20,"maximum":50,"minimum":20,"type":"integer"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://github.com/RosettaCommons/RFdiffusion","tool_id":"rfdiffusion","version":"Base checkpoint release"},{"display_name":"RFdiffusion3","license":"BSD-3-Clause","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"rfdiffusion3.design_all_atom_structures","description":"Generate all-atom protein, protein-small-molecule, ligand-only, or enzyme-scaffold structure proposals with pinned RFdiffusion3 source and an explicit three-dimensional conditioning structure.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"conditioning_structure"}],"capability_id":"rfdiffusion3.design_all_atom_structures","parameters":{"buried_ligand_atoms":[],"design_length_max":1,"design_length_min":1,"exposed_ligand_atoms":[],"fixed_atoms":{},"hbond_acceptors":{},"hbond_donors":{},"hotspots":{},"mode":"<mode>","num_designs":1,"seed":0,"target_segments":[],"unindex":[]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One immutable checksum-bound PDB or mmCIF containing the target, posed ligand, or active-site motif required by the selected mode.","granularity":["selection","dataset_version"],"max_items":1,"media_types":["chemical/x-pdb","chemical/x-mmcif"],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256"],"resource_kinds":["inline"],"role":"conditioning_structure","title":"All-atom conditioning structure"}],"limits":{"design_length_max":600,"design_length_min":20,"max_atom_selections":128,"max_designs":64,"max_structure_bytes":12000000},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Design all-atom structures with RFdiffusion3","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable Dataset of all-atom designs for the selected released mode with source conditioning, sequence, ligand identity where applicable, and structure Artifact evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"generated_structures","title":"RFdiffusion3 all-atom designs"},{"content_schema":null,"dataset_kind":null,"description":"The immutable validated native result, request digest, mode, runtime identity, and artifact inventory.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native RFdiffusion3 result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"buried_ligand_atoms":{"default":[],"description":"Ligand atom names encouraged to remain buried.","items":{"pattern":"^[A-Za-z0-9'_*+-]{1,8}$","type":"string"},"maxItems":128,"title":"Buried ligand atoms","type":"array","uniqueItems":true},"design_length_max":{"description":"Maximum generated design length in residues.","maximum":600,"minimum":20,"title":"Maximum design length","type":"integer"},"design_length_min":{"description":"Minimum generated design length in residues.","maximum":600,"minimum":20,"title":"Minimum design length","type":"integer"},"exposed_ligand_atoms":{"default":[],"description":"Ligand atom names encouraged to remain solvent-exposed.","items":{"pattern":"^[A-Za-z0-9'_*+-]{1,8}$","type":"string"},"maxItems":128,"title":"Exposed ligand atoms","type":"array","uniqueItems":true},"fixed_atoms":{"additionalProperties":{"items":{"pattern":"^[A-Za-z0-9'_*+-]{1,8}$","type":"string"},"maxItems":32,"minItems":1,"type":"array","uniqueItems":true},"default":{},"description":"Residue-to-atom map held fixed during generation.","maxProperties":128,"propertyNames":{"pattern":"^[A-Za-z0-9]{1,4}:[1-9][0-9]{0,5}$"},"title":"Fixed atoms","type":"object"},"hbond_acceptors":{"additionalProperties":{"items":{"pattern":"^[A-Za-z0-9'_*+-]{1,8}$","type":"string"},"maxItems":32,"minItems":1,"type":"array","uniqueItems":true},"default":{},"description":"Residue-to-atom map constrained as hydrogen-bond acceptors.","maxProperties":128,"propertyNames":{"pattern":"^[A-Za-z0-9]{1,4}:[1-9][0-9]{0,5}$"},"title":"Hydrogen-bond acceptors","type":"object"},"hbond_donors":{"additionalProperties":{"items":{"pattern":"^[A-Za-z0-9'_*+-]{1,8}$","type":"string"},"maxItems":32,"minItems":1,"type":"array","uniqueItems":true},"default":{},"description":"Residue-to-atom map constrained as hydrogen-bond donors.","maxProperties":128,"propertyNames":{"pattern":"^[A-Za-z0-9]{1,4}:[1-9][0-9]{0,5}$"},"title":"Hydrogen-bond donors","type":"object"},"hotspots":{"additionalProperties":{"items":{"pattern":"^[A-Za-z0-9'_*+-]{1,8}$","type":"string"},"maxItems":32,"minItems":1,"type":"array","uniqueItems":true},"default":{},"description":"Target residue-to-atom map used as binding hotspots.","maxProperties":128,"propertyNames":{"pattern":"^[A-Za-z0-9]{1,4}:[1-9][0-9]{0,5}$"},"title":"Binding hotspots","type":"object"},"ligand":{"description":"CCD component identifier present in the conditioning structure; required for ligand and enzyme modes.","maxLength":64,"title":"Ligand CCD","type":["string","null"]},"mode":{"description":"RFdiffusion3 generation workflow.","enum":["protein_binder","small_molecule_binder","ligand_only_binder","enzyme_scaffold"],"title":"Design mode","type":"string"},"num_designs":{"default":1,"description":"Number of structures generated in the native batch.","maximum":64,"minimum":1,"title":"Designs","type":"integer"},"seed":{"default":0,"description":"Non-negative deterministic sampling seed.","maximum":2147483647,"minimum":0,"title":"Seed","type":"integer"},"target_segments":{"default":[],"description":"Target chain residue ranges in chain:start-end notation for protein and small-molecule binder modes.","items":{"pattern":"^[A-Za-z0-9]{1,4}:[1-9][0-9]{0,5}-[1-9][0-9]{0,5}$","type":"string"},"maxItems":32,"title":"Target segments","type":"array","uniqueItems":true},"unindex":{"default":[],"description":"Motif residues whose upstream index constraints are removed in enzyme-scaffold mode.","items":{"pattern":"^[A-Za-z0-9]{1,4}:[1-9][0-9]{0,5}$","type":"string"},"maxItems":128,"title":"Unindexed residues","type":"array","uniqueItems":true}},"required":["design_length_min","design_length_max","mode"],"type":"object"},"resource_class":"gpu-small","side_effect_class":"expensive_compute","version":"0.1.0"}],"source_repository":"https://github.com/RosettaCommons/foundry","tool_id":"rfdiffusion3","version":"0.1.0 pinned Foundry profile"},{"display_name":"sanger","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"sanger.align_reference","description":"Align one immutable Sanger consensus against an exact version of an approved nucleotide Reference Library with ranked, coordinate-linked substitution, insertion, and deletion evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"query"},{"resource_id":"<immutable-resource-id>","resource_kind":"reference","role":"references"}],"capability_id":"sanger.align_reference","parameters":{"alignment_mode":"global","quality_column":"quality_scores","query_orientation":"auto","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["alignment","nucleotide_sequences"],"description":"One immutable Dataset Version or frozen Selection containing a nucleotide sequence, normally an assembled Sanger consensus.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"query","title":"Sanger consensus"},{"dataset_kinds":[],"description":"One immutable, checksum-bound nucleotide Reference Library Version resolved by the product.","granularity":["reference_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["reference"],"role":"references","title":"Reference Library Version"}],"limits":{"max_output_bytes_per_role":16777216,"max_references_per_job":100,"max_rows_per_job":1,"max_sequence_length":20000},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Align Sanger consensus to references","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable ranked query-to-reference alignment with coordinate-linked substitutions, insertions, deletions, orientation, quality, and execution evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"reference_alignment","title":"Reference alignment"},{"content_schema":null,"dataset_kind":null,"description":"The immutable versioned native alignment response used for independent conformance and reproducibility.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Sanger reference-alignment result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"alignment_mode":{"default":"global","enum":["global","semiglobal"],"title":"Alignment mode","type":"string"},"quality_column":{"default":"quality_scores","description":"Optional Dataset column containing per-base Phred quality.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Quality column","type":["string","null"]},"query_orientation":{"default":"auto","enum":["auto","forward","reverse"],"title":"Query orientation","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing the nucleotide consensus.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":20000,"max_rows_per_native_batch":20,"mode":"native_batch","native_batch_unit":"groups","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"sanger.assemble_grouped_reads","description":"Group immutable called Sanger reads by an exact dataset field, assemble one evidence-rich contig per group with the released adapter, and transparently partition jobs into ordered native batches of at most 20 groups.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"quality_scores":"<value>","sequence":"<value>","source_checksum_sha256":"<value>","trace_digest_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"chromatograms"}],"capability_id":"sanger.assemble_grouped_reads","parameters":{"group_by_column":"<group_by_column>","max_mismatch_fraction":0.15,"min_consensus_posterior":0.8,"min_overlap":20,"min_trimmed_length":20,"read_overrides":{},"trim_error_probability":0.05,"trim_mode":"mott"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["chromatograms"],"description":"One immutable chromatogram Dataset Version or Selection whose exact grouping field assigns one to four called reads to each assembly.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence","quality_scores","source_checksum_sha256","trace_digest_sha256"],"resource_kinds":["inline"],"role":"chromatograms","title":"Grouped parsed chromatograms"}],"limits":{"max_groups_per_job":5000,"max_groups_per_native_batch":20,"max_output_bytes_per_role":1073741824,"max_reads_per_group":4,"max_rows_per_job":20000,"max_sequence_length":5000},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Assemble grouped Sanger reads","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"One immutable alignment Dataset containing a consensus and complete included/excluded read evidence for every exact input group. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"grouped_assemblies","title":"Grouped Sanger assemblies"},{"content_schema":null,"dataset_kind":null,"description":"The immutable ordered native batch responses, group mapping, individual batch digests, and aggregate product digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native grouped-assembly batches"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"group_by_column":{"description":"Exact dataset column whose non-empty scalar value identifies one independent read group.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Assembly group column","type":"string"},"max_mismatch_fraction":{"default":0.15,"maximum":0.5,"minimum":0.0,"title":"Maximum mismatch fraction","type":"number"},"min_consensus_posterior":{"default":0.8,"maximum":0.999999,"minimum":0.5,"title":"Minimum consensus posterior","type":"number"},"min_overlap":{"default":20,"maximum":5000,"minimum":1,"title":"Minimum read overlap","type":"integer"},"min_trimmed_length":{"default":20,"maximum":5000,"minimum":1,"title":"Minimum trimmed length","type":"integer"},"read_overrides":{"additionalProperties":{"additionalProperties":false,"properties":{"manual_trim_end":{"default":null,"minimum":1,"type":["integer","null"]},"manual_trim_start":{"default":0,"minimum":0,"type":"integer"},"orientation":{"default":"auto","enum":["auto","forward","reverse"],"type":"string"}},"type":"object"},"default":{},"description":"Optional map from immutable logical row ID to reviewed orientation/manual trim bounds.","title":"Per-read orientation and trim overrides","type":"object"},"trim_error_probability":{"default":0.05,"maximum":0.25,"minimum":0.001,"title":"Mott error cutoff","type":"number"},"trim_mode":{"default":"mott","enum":["mott","none"],"title":"Quality trimming","type":"string"}},"required":["group_by_column"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"sanger.assemble_reads","description":"Quality-trim, orient, overlap, and assemble one to four immutable called Sanger reads into a consensus with reconstructable per-column Phred evidence and explicit excluded-read reasons.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"quality_scores":"<value>","sequence":"<value>","source_checksum_sha256":"<value>","trace_digest_sha256":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"chromatograms"}],"capability_id":"sanger.assemble_reads","parameters":{"max_mismatch_fraction":0.15,"min_consensus_posterior":0.8,"min_overlap":20,"min_trimmed_length":20,"read_overrides":{},"trim_error_probability":0.05,"trim_mode":"mott"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["chromatograms"],"description":"One to four immutable chromatogram Dataset Versions or Selections containing called sequence and per-base Phred evidence.","granularity":["selection","dataset_version"],"max_items":4,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence","quality_scores","source_checksum_sha256","trace_digest_sha256"],"resource_kinds":["inline"],"role":"chromatograms","title":"Parsed chromatograms"}],"limits":{"max_output_bytes_per_role":16777216,"max_rows_per_job":1,"max_sequence_length":5000},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Assemble Sanger reads","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"An immutable consensus and equal-length read alignment retaining orientation, trimming, overlap, mismatch, posterior quality, coverage, and per-column source evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"assembled_consensus","title":"Sanger consensus assembly"},{"content_schema":null,"dataset_kind":null,"description":"The immutable versioned assembly response used for independent conformance and reproducibility.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Sanger assembly result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"assembly_id":{"default":null,"description":"Optional stable sample or well identifier; the platform generates one when omitted.","maxLength":200,"minLength":1,"title":"Assembly ID","type":["string","null"]},"max_mismatch_fraction":{"default":0.15,"maximum":0.5,"minimum":0.0,"title":"Maximum mismatch fraction","type":"number"},"min_consensus_posterior":{"default":0.8,"maximum":0.999999,"minimum":0.5,"title":"Minimum consensus posterior","type":"number"},"min_overlap":{"default":20,"maximum":5000,"minimum":1,"title":"Minimum overlap","type":"integer"},"min_trimmed_length":{"default":20,"maximum":5000,"minimum":1,"title":"Minimum trimmed length","type":"integer"},"read_overrides":{"additionalProperties":{"additionalProperties":false,"properties":{"manual_trim_end":{"default":null,"minimum":1,"type":["integer","null"]},"manual_trim_start":{"default":0,"minimum":0,"type":"integer"},"orientation":{"default":"auto","enum":["auto","forward","reverse"],"type":"string"}},"type":"object"},"default":{},"description":"Optional map from immutable logical row ID to reviewed orientation/manual trim bounds.","title":"Per-read orientation and trim overrides","type":"object"},"trim_error_probability":{"default":0.05,"maximum":0.25,"minimum":0.001,"title":"Mott error cutoff","type":"number"},"trim_mode":{"default":"mott","enum":["mott","none"],"title":"Quality trimming","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"sanger.parse_chromatogram","description":"Parse one immutable ABIF/AB1 chromatogram into instrument base calls, Phred quality, base positions, raw A/C/G/T traces, and reviewable secondary-peak evidence without synthetic fallback.","example":{"bindings":[{"resource_id":"<immutable-resource-id>","resource_kind":"asset","role":"chromatogram"}],"capability_id":"sanger.parse_chromatogram","parameters":{"min_primary_signal":1,"secondary_peak_ratio":0.3,"use_iupac":false},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":[],"description":"One immutable Applied Biosystems ABIF/AB1 Asset.","granularity":["asset"],"max_items":1,"media_types":["application/vnd.appliedbiosystems.abif","application/x-abi-chromatogram","application/octet-stream"],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["asset"],"role":"chromatogram","title":"AB1 chromatogram"}],"limits":{"max_input_bytes_per_file":67108864,"max_input_files":1,"max_output_bytes_per_role":268435456},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Parse Sanger chromatogram","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"One immutable chromatogram record containing instrument base calls, per-base Phred quality, base positions, raw A/C/G/T traces, and secondary-peak review evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"chromatogram","title":"Parsed chromatogram"},{"content_schema":null,"dataset_kind":null,"description":"The immutable versioned ABIF parser response used for conformance, review, and reproducibility.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native ABIF parse result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"min_primary_signal":{"default":1,"description":"Do not assess a position whose called-base channel is below this raw signal amplitude.","maximum":1000000,"minimum":1,"title":"Minimum called-base signal","type":"integer"},"secondary_peak_ratio":{"default":0.3,"description":"Minimum signal ratio between the largest non-called channel and the called-base channel at the instrument base position.","maximum":1.0,"minimum":0.05,"title":"Secondary peak ratio","type":"number"},"use_iupac":{"default":false,"description":"Return a separate proposed sequence with flagged two-base mixtures represented by IUPAC codes; never mutate the instrument base calls.","title":"Create IUPAC review sequence","type":"boolean"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"sanger","version":null},{"display_name":"SaProt","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"saprot.embed_protein_sequences","description":"Generate frozen SaProt 650M mean embeddings only for sequences paired with precomputed 3Di structure tokens.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>","structure_3di":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"saprot.embed_protein_sequences","parameters":{"sequence_column":"sequence","structure_3di_column":"structure_3di"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"Exact immutable sequences with precomputed SaProt 3Di tokens; AA-only frozen-model use is rejected.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence","structure_3di"],"resource_kinds":["inline"],"role":"sequences","title":"Structure-aware protein sequences"}],"limits":{"embedding_dimension":1280,"max_rows_per_job":1,"max_sequence_length":1000,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Embed structure-aware protein sequences with SaProt","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset containing the pinned 1,280-dimensional SaProt representation and independently reconstructed binary float digest. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"sequence_embeddings","title":"SaProt structure-aware embeddings"},{"content_schema":null,"dataset_kind":null,"description":"The immutable native embedding contract with exact model-bundle, request, row, vector, and result digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native SaProt embedding result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"},"structure_3di_column":{"default":"structure_3di","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Precomputed 3Di-token column","type":"string"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.1.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"saprot.predict_mutation_effects","description":"Compute upstream-exact SaProt zero-shot mutation log-probability ratios with amino-acid-masked 3Di context and 21-token amino-acid aggregation.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"mutation":"<value>","sequence":"<value>","structure_3di":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"saprot.predict_mutation_effects","parameters":{"mutation_column":"mutation","sequence_column":"sequence","structure_3di_column":"structure_3di"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"Exact immutable sequences with precomputed SaProt 3Di tokens; AA-only frozen-model use is rejected.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence","structure_3di","mutation"],"resource_kinds":["inline"],"role":"sequences","title":"Structure-aware protein sequences"}],"limits":{"max_mutations_per_row":1,"max_rows_per_job":1,"max_sequence_length":1000,"min_rows_per_job":1},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict structure-aware mutation effects with SaProt","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset containing upstream-exact zero-shot log-probability ratios, preserved 3Di context, and 21-token aggregation evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"mutation_effects","title":"SaProt structure-aware mutation effects"},{"content_schema":null,"dataset_kind":null,"description":"The immutable native mutation contract with masked-token identity, wild-type/mutant token blocks, model-bundle identity, and reconstructed digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native SaProt mutation result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"mutation_column":{"default":"mutation","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"One-based mutation column","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"},"structure_3di_column":{"default":"structure_3di","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Precomputed 3Di-token column","type":"string"}},"type":"object"},"resource_class":"memory-large","side_effect_class":"expensive_compute","version":"1.1.0"}],"source_repository":"https://github.com/westlake-repl/SaProt","tool_id":"saprot","version":"SaProt_650M_AF2"},{"display_name":"sequence-design","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.back_translate","description":"Back-translate proteins through a frozen organism codon table with explicit ambiguity and terminal-stop policies.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"design.back_translate","parameters":{"ambiguous_residue_policy":"fail","organism":"human","sequence_column":"sequence","terminal_stop_policy":"preserve"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","alignment"],"description":"A frozen Selection or immutable Dataset Version containing protein sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":100000,"max_total_characters":20000000,"min_rows_per_job":1,"supported_alphabet":"protein_with_x_and_terminal_stop"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Back-translate protein sequences","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Row-preserving DNA derived through the frozen organism codon-table policy. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_sequences","title":"Back-translated DNA sequences"},{"content_schema":null,"dataset_kind":null,"description":"Complete independently verified codon choices, parameters, failures, and result digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native back-translation evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"ambiguous_residue_policy":{"default":"fail","enum":["fail","nnn"],"title":"Ambiguous X residue policy","type":"string"},"organism":{"default":"human","enum":["human","h_sapiens","e_coli","yeast","s_cerevisiae"],"title":"Codon table organism","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Protein sequence column","type":"string"},"terminal_stop_policy":{"default":"preserve","enum":["preserve","remove","require"],"title":"Terminal stop policy","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.codon_optimize","description":"Use pinned DNA Chisel constraints to preserve complete translation, optimize an optional exact region, enforce selected-region GC bounds, freeze flanks, and avoid exact patterns across the complete output on both strands.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"design.codon_optimize","parameters":{"avoid_patterns":[],"gc_max":0.65,"gc_min":0.35,"input_type":"protein","organism":"human","sequence_column":"sequence","terminal_stop_policy":"preserve"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","nucleotide_sequences","annotated_sequences","alignment"],"description":"A frozen Selection or immutable Dataset Version containing protein or coding-DNA sequences, as declared by input_type.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein or coding-DNA sequences"}],"limits":{"max_avoid_patterns":50,"max_rows_per_job":1,"max_sequence_length":100000,"max_total_characters":20000000,"min_rows_per_job":1,"region_coordinates":"optional_paired_one_based_inclusive","supported_alphabet":"protein_or_unambiguous_coding_dna"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Codon-optimize coding sequences","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Complete-translation-conserved DNA with exact selected-region coordinates, frozen-flank/edit-location, selected-region GC, complete-output both-strand pattern, and row-status evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_sequences","title":"Codon-optimized DNA sequences"},{"content_schema":null,"dataset_kind":null,"description":"Complete independently verified DNA Chisel request, normalized region, frozen flanks, constraint evidence, edits, seed, and digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native DNA Chisel evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"avoid_patterns":{"default":[],"items":{"pattern":"^[ACGTacgt]{1,50}$","type":"string"},"maxItems":50,"title":"Exact DNA patterns to avoid on both strands","type":"array","uniqueItems":true},"gc_max":{"default":0.65,"maximum":1,"minimum":0,"title":"Maximum selected-region GC fraction","type":"number","unit":"fraction"},"gc_min":{"default":0.35,"maximum":1,"minimum":0,"title":"Minimum selected-region GC fraction","type":"number","unit":"fraction"},"input_type":{"default":"protein","enum":["protein","coding_dna"],"title":"Input sequence type","type":"string"},"organism":{"default":"human","enum":["human","h_sapiens","e_coli","yeast","s_cerevisiae"],"title":"Expression organism","type":"string"},"region_end":{"default":null,"description":"Pair with region_start. Protein input uses residue positions; coding DNA uses the last base of a complete codon.","maximum":100000,"minimum":1,"title":"Optional region end (one-based, inclusive)","type":["integer","null"]},"region_start":{"default":null,"description":"Pair with region_end. Protein input uses residue positions; coding DNA uses the first base of a complete codon.","maximum":100000,"minimum":1,"title":"Optional region start (one-based, inclusive)","type":["integer","null"]},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Input sequence column","type":"string"},"terminal_stop_policy":{"default":"preserve","enum":["preserve","remove","require"],"title":"Terminal stop policy","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.combinatorial_mutagenesis","description":"Preview and enumerate the complete Cartesian product of declared protein substitutions with explicit wild-type policy, deterministic variant identities, and exact pI and Kyte-Doolittle mean-hydrophobicity deltas.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"design.combinatorial_mutagenesis","parameters":{"max_variants":1000,"mutations":[],"sequence_column":"sequence","wild_type_policy":"exclude"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","alignment"],"description":"A frozen one-row Selection or one-row immutable Dataset Version containing the exact canonical protein source.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"One source protein sequence"}],"limits":{"max_mutagenesis_positions":12,"max_rows_per_job":1,"max_sequence_length":100000,"max_variants":10000,"min_rows_per_job":1,"supported_alphabet":"canonical_protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Build a bounded combinatorial protein library","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"The complete verified Cartesian library with deterministic variant identities, exact sequences, mutations, wild-type policy, and method-labeled pI and mean-hydrophobicity deltas. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"variant_library","title":"Combinatorial protein variant library"},{"content_schema":null,"dataset_kind":null,"description":"Complete independently verified native preview, combination rows, methods, values, identities, and canonical digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native mutagenesis evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"max_variants":{"default":1000,"maximum":10000,"minimum":1,"title":"Execution safety cap","type":"integer"},"mutations":{"description":"Positions are one-based. source_residue must match the immutable source sequence. Each substitutions list excludes wild type.","items":{"additionalProperties":false,"properties":{"position":{"maximum":100000,"minimum":1,"type":"integer"},"source_residue":{"pattern":"^[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]$","type":"string"},"substitutions":{"items":{"pattern":"^[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]$","type":"string"},"maxItems":19,"minItems":1,"type":"array","uniqueItems":true}},"required":["position","source_residue","substitutions"],"type":"object"},"maxItems":12,"minItems":1,"title":"Selected positions and non-WT substitution options","type":"array"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Protein sequence column","type":"string"},"wild_type_policy":{"default":"exclude","description":"include adds the original residue at every selected position, yielding partial mutants and an all-WT variant; exclude mutates every selected position.","enum":["exclude","include"],"title":"Wild-type policy","type":"string"}},"required":["mutations"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.make_insert","description":"Assemble paired or unpaired annotated variable-region protein or coding-DNA sequences as exact leader plus variable plus constant constructs from one approved immutable Reference Library Version, with explicit frame, translation, stop-policy, segment, lineage, and structured-skip evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"},{"resource_id":"<immutable-resource-id>","resource_kind":"reference","role":"reference_library"}],"capability_id":"design.make_insert","parameters":{"constant_references":{},"leader_references":{},"molecule_type":"protein","sequence_column":"sequence","variable_terminal_stop_policy":"fail"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","protein_sequences","annotated_sequences","alignment"],"description":"A frozen Selection or immutable Dataset Version containing exact variable sequences and chain-role annotations, optionally paired by one stable identifier.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Annotated variable-region sequences"},{"dataset_kinds":[],"description":"One exact approved Reference Library Version with checksum-bound leader and constant entries assigned to exact chain roles.","granularity":["reference_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["reference"],"role":"reference_library","title":"Approved construct Reference Library Version"}],"limits":{"junction_policy":"direct_in_frame_concatenation","max_references_per_job":10000,"max_rows_per_job":1,"max_sequence_length":100000,"max_total_characters":20000000,"min_rows_per_job":1,"pairing_policy":"optional_stable_identifier","supported_alphabet":"unambiguous_coding_dna_or_canonical_protein_with_terminal_stop"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Assemble Reference-Library-backed inserts","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing exact leader-variable-constant constructs or structured skips, optional pair IDs, translations, frame evidence, segment checksums, and frozen Reference Library provenance. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_sequences","title":"Reference-backed insert sequences"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native request result with exact reference mappings, stop policy, assembly segments, row digests, and result digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Insert Maker evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_role_column":{"default":null,"description":"Optional exact source column. Auto-detection accepts chain_role or AntPack antpack_chain_type and normalizes H/K/L aliases.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Chain-role column","type":["string","null"]},"constant_references":{"additionalProperties":{"maxLength":200,"minLength":1,"type":"string"},"default":{},"description":"Map normalized chain roles such as heavy, kappa, or lambda to exact constant entry stable IDs in the selected Version.","maxProperties":100,"minProperties":1,"propertyNames":{"pattern":"^.{1,100}$"},"title":"Constant references by chain role","type":"object"},"leader_references":{"additionalProperties":{"maxLength":200,"minLength":1,"type":"string"},"default":{},"description":"Map normalized chain roles such as heavy, kappa, or lambda to exact leader entry stable IDs in the selected Version.","maxProperties":100,"minProperties":1,"propertyNames":{"pattern":"^.{1,100}$"},"title":"Leader references by chain role","type":"object"},"molecule_type":{"default":"protein","enum":["protein","nucleotide"],"title":"Molecule type","type":"string"},"pair_id_column":{"default":null,"description":"Optional stable pairing field. Auto-detection checks pair_id, pairing_key, cell_id, then barcode; unpaired rows remain valid.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Pair identifier column","type":["string","null"]},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Variable sequence column","type":"string"},"variable_terminal_stop_policy":{"default":"fail","description":"fail preserves the row as a structured skip; remove deletes exactly one terminal stop before direct constant-region concatenation.","enum":["fail","remove"],"title":"Variable terminal-stop policy","type":"string"}},"required":["molecule_type","leader_references","constant_references"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.reconstruct_germline","description":"Reconstruct annotated antibody variable regions against one approved immutable Reference Library Version using exact whole-framework replacement, explicit trim alignment, or bounded framework-end replacement. Missing evidence produces row-preserving structured skips; boundaries are never guessed.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"},{"resource_id":"<immutable-resource-id>","resource_kind":"reference","role":"reference_library"}],"capability_id":"design.reconstruct_germline","parameters":{"framework_end_span":15,"method":"whole_framework","molecule_type":"protein","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","protein_sequences","annotated_sequences","alignment"],"description":"A frozen Selection or immutable Dataset Version containing exact source sequences plus germline and coordinate evidence from an annotation workflow.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Annotated variable-region sequences"},{"dataset_kinds":[],"description":"One exact approved Reference Library Version with checksum-bound germline_variable entries, chain roles, and FR1-FR4 coordinates.","granularity":["reference_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":[],"resource_kinds":["reference"],"role":"reference_library","title":"Approved germline Reference Library Version"}],"limits":{"coordinate_system":"one_based_inclusive","max_references_per_job":10000,"max_rows_per_job":1,"max_sequence_length":100000,"max_total_characters":20000000,"min_rows_per_job":1,"supported_alphabet":"unambiguous_coding_dna_or_canonical_protein_with_terminal_stop","trim_alignment":"explicit_forward_ungapped"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Reconstruct exact germline frameworks","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Dataset Version containing exact reconstructed outputs or structured skips, applied segment evidence, translations, normalized chain roles, and frozen Reference Library provenance. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_sequences","title":"Germline-reconstructed sequences"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native request result with exact reference checksums, coordinates, segments, row digests, and result digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native reconstruction evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_role_column":{"default":null,"description":"Optional exact source column. Auto-detection accepts chain_role or AntPack antpack_chain_type and normalizes H/K/L aliases.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Chain-role column","type":["string","null"]},"framework_end_span":{"default":15,"description":"Exact residues or bases replaced at the FR1 5-prime and FR4 3-prime ends. Nucleotide spans must cover complete codons.","maximum":300,"minimum":1,"title":"Framework-end span","type":"integer"},"framework_regions_column":{"default":null,"description":"Optional JSON column with one-based inclusive fr1-fr4 coordinates. Protein AntPack numbering may be converted only when every FR source span is present and contiguous.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Framework-coordinate column","type":["string","null"]},"germline_alignment_column":{"default":null,"description":"JSON column containing forward ungapped equal-span query/reference coordinates and frame 0. Required by trim-based reconstruction; never inferred.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Explicit germline alignment column","type":["string","null"]},"germline_reference_id_column":{"default":null,"description":"Optional exact source column. Auto-detection accepts germline_reference_id or AntPack antpack_v_gene; values must equal frozen reference stable IDs.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Germline stable-ID column","type":["string","null"]},"method":{"default":"whole_framework","enum":["whole_framework","trim_based","framework_ends"],"title":"Reconstruction method","type":"string"},"molecule_type":{"default":"protein","enum":["protein","nucleotide"],"title":"Molecule type","type":"string"},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Source sequence column","type":"string"}},"required":["molecule_type"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"design.reverse_complement","description":"Compute exact IUPAC DNA reverse complements as a complete row-preserving typed result Artifact.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"design.reverse_complement","parameters":{"sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","annotated_sequences","alignment"],"description":"A frozen Selection or immutable Dataset Version containing IUPAC DNA sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Nucleotide sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":100000,"max_total_characters":20000000,"min_rows_per_job":1,"supported_alphabet":"iupac_dna_with_gap"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Reverse-complement nucleotide sequences","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Row-preserving exact IUPAC DNA reverse complements with source identity and structured failures. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"designed_sequences","title":"Reverse-complemented sequences"},{"content_schema":null,"dataset_kind":null,"description":"Complete independently verified native transformation evidence.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native reverse-complement evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"DNA sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"sequence-design","version":null},{"display_name":"structure-analysis","license":null,"minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":500,"max_rows_per_native_batch":500,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"mmseqs.search_binder_reference_sequences","description":"Search a bounded sequence cohort against the versioned Ubi Binder Reference Database. The general design profile combines experimentally confirmed binders with complete UniRef90 protein-space coverage; antibody-specific therapeutic, repertoire, and patent collections remain available through their numbering-aware released methods under the same logical database.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"mmseqs.search_binder_reference_sequences","parameters":{"reference_profile":"confirmed_binders","sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences","comparison"],"description":"One frozen Selection or immutable Dataset Version containing binder or protein sequences. Every bound row is searched as one native cohort.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Sequences to search"}],"limits":{"max_hits_per_collection":50,"max_output_bytes_per_role":50000000,"max_rows_per_job":500,"max_rows_per_native_batch":500,"max_sequence_length":500,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Search the Binder Reference Database","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version with collection-specific nearest hits, exact identity and coverage, threshold decisions, and immutable reference-release evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"binder_reference_matches","title":"Binder Reference Database matches"},{"content_schema":null,"dataset_kind":null,"description":"The complete MMseqs2 cohort response with database release manifests, thresholds, hits, and cryptographic evidence digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native Binder Reference Database evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"reference_profile":{"default":"confirmed_binders","description":"Search the experimentally confirmed binder collection. Complete general protein-space search will be added in a versioned successor after UniRef90 qualification.","enum":["confirmed_binders"],"title":"Reference profile","type":"string"},"sequence_column":{"default":"sequence","description":"Dataset column containing protein sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":20,"max_rows_per_native_batch":20,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"structure_analysis.analyze_structure_interactions","description":"Classify checksum-bound atom contacts with pinned native PDBe Arpeggio, preserving exact source-PDB atom identities, independently recomputable distances, explicit chain-group scope, native provenance, and cryptographic evidence digests.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>","structure_status":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"structure_analysis.analyze_structure_interactions","parameters":{"included_contact_types":["vdw","hbond","weak_hbond","xbond","ionic","metal_complex","aromatic","hydrophobic","carbonyl","polar","weak_polar"]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One frozen Selection or immutable Structures Dataset Version containing checksum-bound PDB rows. Every compatible row is analyzed unless a Selection narrows the input.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_status","structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Structures to analyze"}],"limits":{"max_interactions_per_job":200000,"max_interactions_per_row":50000,"max_output_bytes_per_role":50000000,"max_pdb_bytes_per_job":20000000,"max_pdb_bytes_per_row":5000000,"max_rows_per_job":20,"max_rows_per_native_batch":20,"supported_media_types":["chemical/x-pdb"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Analyze molecular interactions","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Structures Dataset with native contact classifications and independently verified exact source-atom distances for every compatible input row. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"interaction_annotated_structures","title":"Structures with molecular-interaction evidence"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified PDBe Arpeggio response with checksum-bound PDB inputs, Gemmi conversion evidence, native executable provenance, exact atom identities, and cryptographic digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native molecular-interaction evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"chain_group_scopes":{"description":"Optional disjoint chain groups for specific structure rows. Rows without an entry retain contacts between all distinct residues.","items":{"additionalProperties":false,"properties":{"chain_group_a":{"items":{"maxLength":1,"minLength":1,"type":"string"},"maxItems":62,"minItems":1,"title":"First chain group","type":"array","uniqueItems":true},"chain_group_b":{"items":{"maxLength":1,"minLength":1,"type":"string"},"maxItems":62,"minItems":1,"title":"Second chain group","type":"array","uniqueItems":true},"row_id":{"maxLength":200,"minLength":1,"title":"Structure row ID","type":"string"}},"required":["row_id","chain_group_a","chain_group_b"],"type":"object"},"maxItems":20,"title":"Optional row-scoped chain groups","type":"array"},"included_contact_types":{"default":["vdw","hbond","weak_hbond","xbond","ionic","metal_complex","aromatic","hydrophobic","carbonyl","polar","weak_polar"],"description":"Native PDBe Arpeggio classifications retained in the published evidence. Clash, covalent, proximal, and van-der-Waals-clash rows are excluded by default but may be requested explicitly.","items":{"enum":["clash","covalent","vdw_clash","vdw","proximal","hbond","weak_hbond","xbond","ionic","metal_complex","aromatic","hydrophobic","carbonyl","polar","weak_polar"],"type":"string"},"maxItems":15,"minItems":1,"title":"Included native contact types","type":"array","uniqueItems":true}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":100,"max_rows_per_native_batch":100,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"structure_analysis.analyze_structure_surface","description":"Calculate exact residue solvent accessibility and an explicitly heuristic exposed-hydrophobic spatial patch profile from immutable PDB structures; this is surface evidence, not a validated aggregation predictor.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>","structure_status":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"structure_analysis.analyze_structure_surface","parameters":{"exposure_rsa_cutoff":0.25,"hydrophobicity_minimum":1.0,"minimum_patch_residues":2,"patch_distance_angstrom":6.0},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version whose successful rows reference checksum-bound PDB Artifacts.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["structure_status","structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Immutable protein structures"}],"limits":{"max_pdb_bytes_per_job":20000000,"max_pdb_bytes_per_row":5000000,"max_rows_per_job":100,"max_rows_per_native_batch":100,"supported_media_types":["chemical/x-pdb"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Analyze structural surface developability","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A derived immutable Structures Dataset retaining every source row and adding exact FreeSASA residue accessibility plus explicitly heuristic exposed-hydrophobic patch evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"surface_annotated_structures","title":"Surface-annotated structures"},{"content_schema":null,"dataset_kind":null,"description":"The immutable complete structure-surface batch response with checksum-bound inputs, method parameters, residue evidence, patches, and result digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native structural-surface evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"exposure_rsa_cutoff":{"default":0.25,"description":"Minimum residue solvent accessibility relative to the Tien theoretical maximum.","maximum":2,"minimum":0,"title":"Exposed-residue RSA cutoff","type":"number"},"hydrophobicity_minimum":{"default":1.0,"description":"Minimum Kyte-Doolittle residue hydrophobicity for patch-candidate membership.","maximum":4.5,"minimum":-4.5,"title":"Hydrophobicity cutoff","type":"number"},"minimum_patch_residues":{"default":2,"description":"Minimum connected residue count required to publish a patch hotspot.","maximum":20,"minimum":2,"title":"Minimum patch residues","type":"integer"},"patch_distance_angstrom":{"default":6.0,"description":"Maximum minimum heavy-atom distance connecting two exposed hydrophobic residues.","exclusiveMinimum":0,"maximum":20,"title":"Patch connectivity distance (Å)","type":"number"}},"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"structure_analysis.calculate_protein_properties","description":"Calculate exact average and monoisotopic mass, pI, extinction, instability, aliphatic index, GRAVY, aromaticity, and residue-linked Kyte-Doolittle evidence with explicit range, DNA translation, and paired-chain semantics.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"structure_analysis.calculate_protein_properties","parameters":{"custom_extinction_delta_molar":0,"custom_mass_delta_da":0,"hydrophobicity_scale":"kyte_doolittle","hydrophobicity_window":9,"input_molecule_type":"protein","pair_mode":"separate_components","sequence_column":"sequence","translation_frame":1,"translation_table":1},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["nucleotide_sequences","protein_sequences","annotated_sequences","comparison"],"description":"A frozen Selection or immutable Dataset Version containing one primary sequence and optional partner/range evidence per row.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Protein or coding-DNA sequences"}],"limits":{"max_dna_characters":3000000,"max_protein_profile_points":1000000,"max_rows_per_job":1,"max_sequence_length":6000,"supported_alphabet":"standard_protein_or_unambiguous_dna"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Calculate protein physicochemical properties","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A complete typed result Artifact retaining every source row with exact scalar, paired-component, range, and residue-linked hydrophobicity evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"property_annotated_sequences","title":"Physicochemical property-annotated sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable complete Biopython ProtParam batch response used for independent verification and reproducibility.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native physicochemical evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"custom_extinction_delta_molar":{"default":0,"maximum":1000000000,"minimum":-1000000000,"title":"Aggregate custom extinction delta (M⁻¹ cm⁻¹)","type":"integer"},"custom_mass_delta_da":{"default":0,"maximum":1000000,"minimum":-1000000,"title":"Aggregate custom mass delta (Da)","type":"number"},"hydrophobicity_scale":{"default":"kyte_doolittle","enum":["kyte_doolittle"],"title":"Hydrophobicity scale","type":"string"},"hydrophobicity_window":{"default":9,"description":"Odd window width; edge positions use the available clipped window.","maximum":51,"minimum":1,"title":"Centered hydrophobicity window","type":"integer"},"input_molecule_type":{"default":"protein","enum":["protein","dna"],"title":"Input molecule type","type":"string"},"label_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional row label column","type":["string","null"]},"pair_mode":{"default":"separate_components","enum":["separate_components","concatenated"],"title":"Partner interpretation","type":"string"},"partner_ranges_column":{"default":null,"description":"JSON list of one-based inclusive translated-protein ranges.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional partner protein ranges column","type":["string","null"]},"partner_sequence_column":{"default":null,"pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional partner sequence column","type":["string","null"]},"ranges_column":{"default":null,"description":"JSON list of one-based inclusive translated-protein ranges.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Optional primary protein ranges column","type":["string","null"]},"sequence_column":{"default":"sequence","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Primary sequence column","type":"string"},"translation_frame":{"default":1,"maximum":3,"minimum":1,"title":"DNA translation frame","type":"integer"},"translation_table":{"default":1,"enum":[1],"title":"DNA translation table","type":"integer"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":20,"max_rows_per_native_batch":20,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"structure_analysis.compare_structures","description":"Rigidly superpose two to twenty checksum-bound PDB structures against one explicit reference using exact chain/residue/insertion C-alpha correspondence, with global RMSD, residue displacement, unmatched-residue, transformation, and real superposition-PDB evidence.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>","structure_status":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"structure_analysis.compare_structures","parameters":{"reference_row_id":"<reference_row_id>"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One frozen Selection or immutable Structures Dataset Version containing the explicit reference row and one to nineteen compatible target PDB rows.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_status","structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Structures to compare"}],"limits":{"max_output_bytes_per_role":50000000,"max_pdb_bytes_per_job":20000000,"max_pdb_bytes_per_row":5000000,"max_rows_per_job":20,"max_rows_per_native_batch":20,"min_rows_per_job":2,"supported_media_types":["chemical/x-pdb"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Compare protein structures by exact residue identity","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"One immutable comparison row per target with exact Kabsch metrics, residue displacement, unmatched-residue evidence, and an authorized real superposition PDB Artifact. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"structure_comparisons","title":"Structure comparison evidence"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified comparison response with checksum-bound source PDBs, transforms, residue evidence, superposition bytes, and cryptographic digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native structure-comparison evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"reference_row_id":{"description":"Exact logical row ID of the structure used as the fixed Kabsch reference.","maxLength":200,"minLength":1,"title":"Reference structure row","type":"string"}},"required":["reference_row_id"],"type":"object"},"resource_class":"cpu-medium","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"structure_analysis.detect_liability_motifs","description":"Scan antibody protein sequences for paper-backed LAP liability motifs with optional CDR, residue-exposure, germline, and approved-therapeutic prevalence context.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"sequence":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"sequences"}],"capability_id":"structure_analysis.detect_liability_motifs","parameters":{"buried_rsa_cutoff":0.25,"cdr_boundary_residues":1,"sequence_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing antibody protein sequences.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["sequence"],"resource_kinds":["inline"],"role":"sequences","title":"Antibody sequences"}],"limits":{"max_rows_per_job":1,"max_sequence_length":2000,"supported_alphabet":"protein"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Detect antibody liability motifs","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A complete typed result Artifact retaining source fields and normalized LAP liability counts, hits, warnings, and evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"annotated_sequences","title":"Liability-annotated sequences"},{"content_schema":null,"dataset_kind":null,"description":"The immutable per-row Structure Analysis responses used for conformance and reproducibility.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native liability result"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"buried_rsa_cutoff":{"default":0.25,"description":"Relative solvent accessibility threshold used to flag buried liabilities.","maximum":1,"minimum":0,"title":"Buried RSA cutoff","type":"number"},"cdr_boundary_residues":{"default":1,"description":"Residues outside each declared CDR included in CDR-scoped motif evaluation.","maximum":3,"minimum":0,"title":"CDR boundary residues","type":"integer"},"cdr_ranges_column":{"default":null,"description":"Optional JSON column of one-based named CDR ranges.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"CDR ranges column","type":["string","null"]},"germline_sequence_column":{"default":null,"description":"Optional protein-sequence column used to flag liabilities already present in the germline.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Germline sequence column","type":["string","null"]},"residue_context_column":{"default":null,"description":"Optional JSON column containing IMGT, region, exposure, and chain context by sequence position.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Residue context column","type":["string","null"]},"sequence_column":{"default":"sequence","description":"Dataset column containing amino-acid sequences.","pattern":"^[a-z][a-z0-9_]{0,63}$","title":"Sequence column","type":"string"}},"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.2.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":100,"max_rows_per_native_batch":100,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"structure_analysis.measure_structure_geometry","description":"Measure checksum-bound atom-to-atom distances, three-atom angles, and signed four-atom dihedrals from immutable PDB structures using explicit primary-conformer atom identities and row-scoped measurement IDs.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>","structure_status":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"structure_analysis.measure_structure_geometry","parameters":{"measurements":[]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"One frozen Selection or immutable Structures Dataset Version containing every checksum-bound PDB row named by the measurement definitions.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_status","structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Structures to measure"}],"limits":{"max_measurements_per_job":10000,"max_measurements_per_row":100,"max_output_bytes_per_role":50000000,"max_pdb_bytes_per_job":20000000,"max_pdb_bytes_per_row":5000000,"max_rows_per_job":100,"max_rows_per_native_batch":100,"supported_media_types":["chemical/x-pdb"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Measure exact structure geometry","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving immutable Structures Dataset with independently verified distance, angle, and signed-dihedral evidence attached to each requested source row. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"measured_structures","title":"Structures with exact geometry evidence"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified native measurement response with checksum-bound PDB inputs, exact atom evidence, method conventions, and cryptographic digests.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Native structure-geometry evidence"}],"parameters_schema":{"$defs":{"atom_selector":{"additionalProperties":false,"properties":{"atom_name":{"maxLength":4,"minLength":1,"title":"Atom name","type":"string"},"chain_id":{"description":"Exact one-character PDB chain ID; use _ for a blank chain.","maxLength":1,"minLength":1,"title":"Chain ID","type":"string"},"insertion_code":{"default":"","maxLength":1,"title":"Insertion code","type":"string"},"record_type":{"enum":["ATOM","HETATM"],"title":"PDB record type","type":"string"},"residue_name":{"maxLength":3,"minLength":1,"title":"Residue name","type":"string"},"residue_number":{"maximum":9999,"minimum":-999,"title":"Residue number","type":"integer"}},"required":["chain_id","residue_number","atom_name"],"type":"object"}},"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"measurements":{"description":"Row-scoped measurement definitions. Atom order determines the second-atom angle vertex and signed four-atom dihedral convention.","items":{"additionalProperties":false,"allOf":[{"if":{"properties":{"measurement_type":{"const":"distance"}},"required":["measurement_type"]},"then":{"properties":{"atoms":{"maxItems":2,"minItems":2}}}},{"if":{"properties":{"measurement_type":{"const":"angle"}},"required":["measurement_type"]},"then":{"properties":{"atoms":{"maxItems":3,"minItems":3}}}},{"if":{"properties":{"measurement_type":{"const":"dihedral"}},"required":["measurement_type"]},"then":{"properties":{"atoms":{"maxItems":4,"minItems":4}}}}],"properties":{"atoms":{"items":{"$ref":"#/$defs/atom_selector"},"maxItems":4,"minItems":2,"title":"Ordered atom selectors","type":"array"},"measurement_id":{"maxLength":200,"minLength":1,"title":"Measurement ID","type":"string"},"measurement_type":{"enum":["distance","angle","dihedral"],"title":"Measurement type","type":"string"},"row_id":{"maxLength":200,"minLength":1,"title":"Structure row ID","type":"string"}},"required":["row_id","measurement_id","measurement_type","atoms"],"type":"object"},"maxItems":10000,"minItems":1,"title":"Exact structure measurements","type":"array"}},"required":["measurements"],"type":"object"},"resource_class":"cpu-small","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":null,"tool_id":"structure-analysis","version":null},{"display_name":"Structure Utilities","license":"MIT","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":200,"max_rows_per_native_batch":200,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_collective","successful_items_preserved":false},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"structure_utilities.calculate_rmsd_matrix","description":"Calculate and durably publish a condensed pairwise RMSD matrix for an exactly atom-corresponded PDB ensemble with pyRMSD's original serial QCP C++ kernel.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"structure_utilities.calculate_rmsd_matrix","parameters":{"algorithm":"qcp_serial","atom_selection":"ca","chain_ids":[]},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version containing two or more checksum-bound PDB Artifacts with identical ordered atom identities after selection.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Aligned structure ensemble"}],"limits":{"max_input_pdb_bytes_per_row":5000000,"max_pair_count":19900,"max_rows_per_job":200,"max_rows_per_native_batch":200,"max_selected_atoms_per_structure":100000,"max_total_input_pdb_bytes":20000000,"min_rows_per_job":2,"supported_format":"pdb"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Calculate an ensemble RMSD matrix with pyRMSD","outputs":[{"content_schema":null,"dataset_kind":null,"description":"A checksum-bound condensed matrix with every ordered structure pair, RMSD in angstroms, selected atom count, and atom-identity digest.","media_type":"application/json","resource_kind":"artifact","role":"rmsd_matrix","title":"pyRMSD pairwise RMSD matrix"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified QCP response, source checksums, method identity, parameters, and response digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"pyRMSD native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"algorithm":{"const":"qcp_serial","default":"qcp_serial","title":"RMSD algorithm","type":"string"},"atom_selection":{"default":"ca","enum":["ca","backbone","all_heavy"],"title":"Atom selection","type":"string"},"chain_ids":{"default":[],"items":{"maxLength":1,"minLength":1,"type":"string"},"maxItems":100,"title":"PDB chain IDs","type":"array","uniqueItems":true}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":1,"max_rows_per_native_batch":1,"mode":"single_input","partial_failure_semantics":{"failed_items":"terminal_job_error","mode":"atomic_single_input","successful_items_preserved":false},"qualification":"native_batch_not_demonstrated"},"capability_id":"structure_utilities.repair_structures","description":"Repair checksum-bound PDB structures with PDBFixer, including bounded missing-residue handling, nonstandard-residue replacement, heterogen policy, missing atoms, and optional hydrogens, then publish verified PDB Artifacts and a derived Structures Dataset.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_size_bytes":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"structure_utilities.repair_structures","parameters":{"add_hydrogens":true,"add_missing_atoms":true,"add_missing_residues":false,"heterogen_policy":"keep_water","missing_atom_seed":0,"ph":7.0,"replace_nonstandard_residues":true},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version whose rows reference checksum-bound PDB Artifacts.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["structure_artifact_id","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Structures to repair"}],"limits":{"max_declared_missing_residues":100,"max_input_pdb_bytes_per_row":5000000,"max_rows_per_job":1,"max_total_input_pdb_bytes":20000000,"min_rows_per_job":1,"supported_format":"pdb"},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Repair PDB structures with PDBFixer","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Structures Dataset whose successful rows reference checksum-verified repaired PDB Artifacts and explicit repair evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"repaired_structures","title":"PDBFixer repaired Structures Dataset"},{"content_schema":null,"dataset_kind":null,"description":"The complete independently verified repair response, method identity, parameters, counts, and response digest.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"PDBFixer native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"add_hydrogens":{"default":true,"title":"Add hydrogens","type":"boolean"},"add_missing_atoms":{"default":true,"title":"Add missing atoms","type":"boolean"},"add_missing_residues":{"default":false,"description":"Add declared missing residues, up to the released limit. Disabled by default because loop geometry is modeled rather than observed.","title":"Add missing residues","type":"boolean"},"heterogen_policy":{"default":"keep_water","enum":["remove_all","keep_water","keep_all"],"title":"Heterogen policy","type":"string"},"missing_atom_seed":{"default":0,"maximum":2147483647,"minimum":0,"title":"Missing-atom placement seed","type":"integer"},"ph":{"default":7.0,"maximum":14.0,"minimum":0.0,"title":"Hydrogen-addition pH","type":"number"},"replace_nonstandard_residues":{"default":true,"title":"Replace recognized nonstandard residues","type":"boolean"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/openmm/pdbfixer; https://github.com/victor-gil-sepulveda/pyRMSD","tool_id":"structure-utilities","version":"PDBFixer 1.12.0; pyRMSD 4.2.1"},{"display_name":"SwiftMHC","license":"Apache-2.0","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":64,"max_rows_per_native_batch":64,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"swiftmhc.predict_peptide_mhc","description":"Predict the published unitless SwiftMHC transformed-affinity score and optional unrefined peptide–MHC-I structure for bounded batches of canonical HLA-A*02:01 9-mers on the exact qualified CPU image.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"peptide":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"peptides"}],"capability_id":"swiftmhc.predict_peptide_mhc","parameters":{"allele":"HLA-A*02:01","output_mode":"binder_structures","peptide_column":"sequence"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["protein_sequences","annotated_sequences"],"description":"A frozen Selection or immutable Dataset Version containing one row per canonical 9-mer peptide.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":true,"required":true,"required_fields":["peptide"],"resource_kinds":["inline"],"role":"peptides","title":"HLA-A*02:01 9-mer peptides"}],"limits":{"max_native_batch_size":64,"max_rows_per_job":64,"min_rows_per_job":1,"supported_alleles":["HLA-A*02:01"],"supported_peptide_lengths":[9]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Predict HLA-A*02:01 peptide binding and structure with SwiftMHC","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"A row-preserving Dataset Version with transformed-affinity scores, binder calls, structure Artifact references, and exact release evidence. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"pmhc_predictions","title":"SwiftMHC peptide–MHC predictions"},{"content_schema":null,"dataset_kind":null,"description":"The checksum-verified native response and runtime identity.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"SwiftMHC native evidence"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"allele":{"const":"HLA-A*02:01","default":"HLA-A*02:01","description":"The only allele supported by the released checkpoint.","title":"MHC-I allele","type":"string"},"output_mode":{"default":"binder_structures","description":"Return affinity only, structures for predicted binders, or structures for every row. Structures are not energy-minimized.","enum":["affinity_only","binder_structures","all_structures"],"title":"Structure output","type":"string"},"peptide_column":{"default":"sequence","description":"Dataset column containing exactly nine canonical amino acids.","minLength":1,"title":"Peptide column","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/X-lab-3D/swiftmhc-inference","tool_id":"swiftmhc","version":"1.0.0"},{"display_name":"Ubi Develop","license":"Feature-profile implementation and FreeSASA MIT; BioPhi MIT with OASis CC-BY-4.0 data; NanoShaper GPL-3.0-or-later as a separate internal service","minimum_plan":"free","operations":[{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":4,"max_rows_per_native_batch":4,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"ubi_develop.assess_antibody_developability","description":"Compute 24 interpretable AbDevelop-derived antibody developability features from exact VH/VL sequences and a checksum-bound structure, using qualified BioPhi OASis and NanoShaper v1.2 dependencies; assay predictions are explicitly withheld.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"heavy_chain":"<value>","heavy_chain_subtype":"<value>","light_chain":"<value>","light_chain_subtype":"<value>","structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>","structure_status":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"ubi_develop.assess_antibody_developability","parameters":{"numbering_scheme":"imgt"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version with exact heavy/light sequences, chain subtypes, and checksum-bound H/L antibody PDB Artifacts.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["heavy_chain","light_chain","heavy_chain_subtype","light_chain_subtype","structure_status","structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"Paired antibody sequences and structures"}],"limits":{"max_pdb_bytes_per_job":8000000,"max_pdb_bytes_per_row":2000000,"max_rows_per_job":4,"max_rows_per_native_batch":4,"max_sequence_length":180,"min_rows_per_job":1,"supported_media_types":["chemical/x-pdb"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Profile antibody developability with Ubi Develop","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Twenty-four developability descriptors, chain humanness values, and IMGT-aware sequence liabilities for each antibody. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"developability_profiled_structures","title":"Developability profile results"},{"content_schema":null,"dataset_kind":null,"description":"Complete per-antibody descriptor, humanness, and sequence-liability results in JSON format.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Downloadable developability results"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"numbering_scheme":{"const":"imgt","default":"imgt","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.2.1"},{"approval_policy":"organization_policy","availability":{"qualified":true,"released":true,"status":"available"},"batch":{"client_side_loops":false,"max_rows_per_job":10,"max_rows_per_native_batch":10,"mode":"native_batch","native_batch_unit":"rows","partial_failure_semantics":{"failed_items":"reported_within_batch_result","mode":"structured_per_item","successful_items_preserved":true},"qualification":"released_manifest_native_batch_evidence"},"capability_id":"ubi_develop.assess_static_trp_oxidation_risk","description":"Screen CDR tryptophan sites in checksum-bound IMGT-numbered antibody PDBs with a transparent paper-inspired static SASA and APBS electrostatics rule; this is a research heuristic, not the unreleased AbDevelop or source-paper model.","example":{"bindings":[{"inline_value":{"rows":[{"logical_row_id":"input-1","values":{"structure_artifact_id":"<value>","structure_checksum_sha256":"<value>","structure_media_type":"<value>","structure_size_bytes":"<value>","structure_status":"<value>"}}],"schema":"ubi.inline-rows/v1"},"resource_kind":"inline","role":"structures"}],"capability_id":"ubi_develop.assess_static_trp_oxidation_risk","parameters":{"numbering_scheme":"imgt"},"project_id":"<project-id>"},"http":{"artifacts":"/api/v1/jobs/{job_id}/artifacts","job":"/api/v1/jobs/{job_id}","preview":"/api/v1/runs/preview","submission_requirements":{"body_fields":["expected_preview_digest","preview_receipt"],"exact_preview_request_required":true,"headers":["Authorization","Idempotency-Key"]},"submit":"/api/v1/runs"},"input_roles":[{"dataset_kinds":["structures"],"description":"A frozen Selection or immutable Structures Dataset Version whose successful rows reference checksum-bound H/L antibody PDB Artifacts asserted to use IMGT numbering.","granularity":["selection","dataset_version"],"max_items":1,"media_types":[],"min_items":1,"ordered":false,"required":true,"required_fields":["structure_status","structure_artifact_id","structure_media_type","structure_checksum_sha256","structure_size_bytes"],"resource_kinds":["inline"],"role":"structures","title":"IMGT-numbered antibody structures"}],"limits":{"max_pdb_bytes_per_job":20000000,"max_pdb_bytes_per_row":2000000,"max_rows_per_job":10,"max_rows_per_native_batch":10,"min_rows_per_job":1,"supported_media_types":["chemical/x-pdb"]},"mcp":{"preview":"preview_capability_run","status":"get_job","submit":"submit_capability_run"},"name":"Screen static tryptophan oxidation risk with Ubi Develop","outputs":[{"content_schema":"ubi.scientific-tabular-result/v1","dataset_kind":null,"description":"Antibody structures annotated with residue-level SASA, electrostatic potential, and Trp risk calls. Returned as one complete typed result Artifact; persistence as a Dataset requires an explicit Save action.","media_type":"application/json","resource_kind":"artifact","role":"trp_oxidation_annotated_structures","title":"Static Trp-risk results"},{"content_schema":null,"dataset_kind":null,"description":"Complete per-site SASA, electrostatic-potential, and risk-call results in JSON format.","media_type":"application/json","resource_kind":"artifact","role":"native_result","title":"Downloadable Trp-site results"}],"parameters_schema":{"$schema":"https://json-schema.org/draft/2020-12/schema","additionalProperties":false,"properties":{"numbering_scheme":{"const":"imgt","default":"imgt","description":"The current site-selection contract requires H/L chains numbered with IMGT residue identifiers.","type":"string"}},"type":"object"},"resource_class":"cpu-large","side_effect_class":"expensive_compute","version":"1.0.0"}],"source_repository":"https://github.com/xunfold/AbDevelop","tool_id":"ubi-develop","version":"feature profile 1.2.1; static Trp heuristic 1.0.0"}]}
