mims-harvard/tooluniverse/templates

ToolUniverse Research

Brings ToolUniverse's 2500+ scientific tools and 133 structured research workflows into Claude Science. The tooluniverse PyPI package supplies the tools; this skill bundles the workflows and a kernel sidecar that wires them up.

Setup

Run all cells in the `tooluniverse` conda environment. Loading this skill auto-defines these helpers in the kernel:

• get_tu() → a loaded ToolUniverse instance (cache redirected to the workspace, since ~/.tooluniverse is read-only here).
• tu_workflows() → list all 133 workflows (name + description).
• find_tu_workflow(query) → rank workflows by relevance to a question.
• tu_workflow(name) → the full step-by-step procedure for one workflow.
• tu_tool_info(tu, name) → a tool's JSON spec, including its argument schema.

Answering a research question

1. Route to a workflow: find_tu_workflow("tell me about metformin") returns ranked names. (Or browse tu_workflows().)
2. Load its procedure: print(tu_workflow("tooluniverse-drug-research")) and follow the steps.
3. Execute the tools the workflow names. Every ToolName(args) reference maps to:

``python tu = get_tu() tu.run({"name": "PubChem_get_CID_by_compound_name", "arguments": {"name": "metformin"}}) ``

1. Confirm argument names before a call if unsure — tu_tool_info(tu, "PubChem_get_CID_by_compound_name") shows the exact schema. Workflow prose abbreviates arguments; the schema is authoritative.
2. Discover tools at runtime when no workflow fits:

``python tu.run({"name": "Tool_Finder_Keyword", "arguments": {"description": "drug adverse events", "limit": 10}}) ``

Notes

• Most tools work without API keys. A few (NCBI, OncoKB, NVIDIA, …) unlock enhanced access when keys are set in the env — add under Customize → Credentials, then expose them in the tooluniverse env.
• Workflows are self-contained: report templates, checklists, and tool references are appended to each as appendices.
• These workflows emphasize looking things up over recalling them — when a workflow says query a database, run the tool rather than answering from memory.