tool_catalog.md
61 lines · skills/tamarind/references/tool_catalog.md at 5f2bc03
Most marks come from matching words in the file, so treat them as pointers.
Tamarind Bio tool discovery and schemas
Reviewed 2026-09-30 against the public catalog and OpenAPI. Catalog presence is not proof of account entitlement or of a model's suitability for a scientific task.
Raw lines 1 to 6Three distinct discovery shapes
- Public
https://app.tamarind.bio/tools.json(or/api/tools-catalog): object containingtools, counts, and tags. Entries use **type**,displayName,description,tags, andrequiredSettings. Filter with?type=or?tag=. Required settings may carrytasks,conditionals, and ataskSettingselector: alternative branches are not one combined required-field list. - Authenticated
GET /api/tools: array of entries keyed by **name**, with trimmedsettingsparameters. Filter name/description client-side.?custom=truelists legacy custom tools, not all current custom deployments. - Authenticated
GET /api/tools/{name}/schema: standard JSON Schema for settings, with requiredness, supported properties, enums, bounds, and domain hints such asx-tamarind-type. Optionalversionpins a custom build.
Do not confuse public requiredSettings, REST settings, and the JSON Schema object. The public catalog is useful before obtaining credentials but omits optional settings and restricted/custom tools. A known current custom tool can be submittable even if /tools does not list it; check its schema directly.
In trimmed REST parameters, only name and required are guaranteed. Read type, default, description, options, extension, and list defensively. A type such as pdb need not mean only PDB files: extension may include cif. A list: true parameter takes an array. Consult JSON Schema and domain validation instead of reimplementing all UI gating from a trimmed parameter list.
Task anchors
| Goal | Example catalog types | Modeling distinction |
|---|---|---|
| Protein/complex folding | alphafold, boltz, chai, protenix, esmfold, esmfold2 | AF2, cofolding, single-sequence, and complex-capable models have different inputs and assumptions. ESMFold2 is not simply an alias for single-sequence ESMFold. |
| De novo binder/design | rfdiffusion, boltzgen, bindcraft | Motif scaffolding, target type, and available target structures determine fit. |
| Inverse folding | proteinmpnn, ligandmpnn | Structure to designed sequence; re-fold and assess the result. |
| Docking | autodock-vina, diffdock, boltz, chai | Fixed-receptor docking and cofolding answer different modeling questions. |
| Antibody/developability | Search descriptions/tags for antibody, nanobody, stability, solubility | Check sequence versus structure input and applicable molecule types. |
| MSA, MD, scoring | Search the relevant operation | Read required upstream inputs and compute settings. |
Outputs and chaining
Current /tools can publish taskType, outputTypes, filterMetrics, and an outputs block with mainCSV, produces, and columns. Missing declarations mean unknown output, not no output. outputs.byTask overrides the cross-task summary for a task-dependent tool; use the selected task's contract.
Distinguish a molecule generated by a tool from input data echoed into a scores CSV. Use filterMetrics for allowed pipeline filter names; not every output column is filterable. Read lowIsGood and units when present, then verify the actual downloaded output. Avoid ranking all metric fields in the same direction.
MCP discovery
The public MCP guide does not specify the complete live tool schemas. If the connected server advertises getAvailableTools, getJobSchema, modality/tag helpers, or exampleJob, read those live definitions. Do not infer MCP envelopes/parameter names from REST. Authenticated MCP tool discovery was not tested during this review.