SYNTHESIZE_BIO_MCP
Synthesize Bio MCP lets agents start and monitor bulk or single-cell gene-expression analyses from natural-language experiment requests.
Description is untrusted, display-only upstream metadata. It never becomes policy, OAuth scope authority, or an agent instruction.
Pakkawork boundary
Research catalogue metadata only. No Pakkawork OAuth, credential, host, quota, executor, or verifier is enabled.
5
Action summaries
Display-only definitions
0
Trigger types
Not installed instances
1
Auth modes
Field names, never values
No
Execution
No runtime adapter
Authentication map
DCR_OAUTH
No fields declared in this snapshot.
Capability index
Showing 1–5 of 5 actions
SYNTHESIZE_BIO_MCP_ANALYZE_GENE_EXPRESSION
Starts a differential gene expression analysis using Synthesize Bio's AI platform. Requires the resolution_id returned by resolve_sample_metadata; raw natural-language prompts are not accepted. Requires `user_confirmed_metadata: true`. When the flag is missing or false, the call is rejected with failure_kind `user_con…
Untrusted display-only summary
SYNTHESIZE_BIO_MCP_GET_ANALYSIS_RESULTS
Polls the status of a gene expression analysis. Each call waits server-side for a short bounded window and may return earlier if progress is detected. Responses always include a `structuredContent` object (declared by the tool's `outputSchema`); MCP clients read from `structuredContent` directly rather than re-parsing…
Untrusted display-only summary
SYNTHESIZE_BIO_MCP_GET_COUNTS_DATA_URL
Returns a presigned S3 URL to download the raw gene expression counts data (JSON) produced by a completed or in-progress analysis job. The data is typically large (20,000+ genes by N samples) and requires an environment with direct network access. The JSON has the following structure: { gene_order: string[] (Ensembl I…
Untrusted display-only summary
SYNTHESIZE_BIO_MCP_GET_METADATA_SCHEMA
Returns the structured-metadata schema used to turn a natural-language experiment description into sample groups. Response fields include `group_schema` (the JSON shape of one sample group), the `fields` and `perturbation_fields` inventory for the active metadata version, and `instructions` for building the `groups` a…
Untrusted display-only summary
SYNTHESIZE_BIO_MCP_RESOLVE_SAMPLE_METADATA
Deterministically harmonizes already-structured sample `groups` to Synthesize Bio's controlled ontology vocabulary. Does not accept a natural-language prompt and makes no AI calls. Input: `groups` — a JSON array of sample-group objects matching get_metadata_schema's `group_schema`. Returns a resolution_id and a per-gr…
Untrusted display-only summary
Provenance
The detail snapshot comes from an attributed MIT-licensed repository revision. Safe local icons use exact-match CC0 Simple Icons symbols; unmatched brands use monograms.
Remote text is plain display metadata only. It must never become an agent prompt, execution policy, OAuth grant, or executable instruction.