mirror of
https://github.com/mims-harvard/ToolUniverse.git
synced 2026-09-19 07:31:47 +08:00
Shanghua Gao
08246bcd4d
* docs: expand redirect map with 15 additional legacy paths Adds redirects for paths uncovered in a second-pass audit against the live published site. Each destination verified to return HTTP 200 on https://zitniklab.hms.harvard.edu/ToolUniverse/. New /tutorials/ → /guide/, /tools/, /expand_tooluniverse/ redirects: - make_your_data_searchable, make_your_data_agent_searchable, build_search_and_share_datastores → guide/make_your_data_agent_searchable - skills → guide/skills_showcase - tool_finder → guide/finding_tools - overview → guide/index - remote_tools → tools/remote_tools - mcp_integration → expand_tooluniverse/remote_tools/mcp_integration Top-level legacy pages (404 at root, now redirected): - getting_started → guide/python_guide - deployment, contributing, changelog → about/<page> - faq → help/faq Local build confirms all 22 redirect stubs generate and that every destination file exists in the build output. * docs: fix broken sphinx-tabs, dead toctrees, orphan pages, missing image Build now produces 0 warnings/errors of these structural categories (down from ~280 such issues): - Re-enable sphinx_tabs.tabs extension (3.5.0 supports Sphinx 9.x); fixes 7 broken "Unknown directive type tabs" errors that made help/faq.html and help/troubleshooting.html render incomplete. - Drop 25+ dead toctree entries in api/modules.rst and api/tooluniverse.rst that referenced per-module pages never generated by sphinx-apidoc; modules.rst now points at the existing comprehensive tooluniverse autodoc page. - Wire 16 orphan pages into the master toctree so they're reachable from the navigation, including tooluniverse_case_study, visualization_tutorial, expert_feedback, literature_search_web_ui, euhealth, logging, openrouter, streaming, vllm, wechat_community, simbad_tools, the guide/index landing page, and the full expand_tooluniverse sub-tree. - Remove three stale ":doc:" links to old/{quickstart,installation, getting_started} from sitemap.rst (those directories are excluded from the build) and mark sitemap.rst as :orphan: since it's a parallel nav surface by design. - Mark MCP_TASKS_GUIDE.md as orphan and exclude the internal DOCUMENTATION_STRUCTURE.md meta-doc from the build. - Add the missing tools/remote/ui.jpg referenced by the remote expert_feedback page (previously: broken image). * docs: eliminate all 49 structural Sphinx ERRORs (broken tables, directives, headings) Round-3 build cleanup. Builds now finish with 0 structural ERRORs of any category (previous: 49 ERRORs spread across 20 files). Total warnings/errors dropped from 280 → 114; the remaining 114 are all in Python source-file docstrings (out of scope for a docs PR). Categories fixed: **Malformed tables** (8 files) Replace ASCII grid tables with mis-aligned pipes and inline-markdown pipe tables (which RST mis-parses as substitution references) with ``list-table`` directives that render correctly across all themes: - guide/literature_search_tools_tutorial.rst (two tables) - guide/cache_system.rst (env-var table whose first column overflowed) - guide/clinical_guidelines_tools.rst - guide/make_your_data_agent_searchable.rst - expand_tooluniverse/contributing/index.rst - expand_tooluniverse/contributing/remote_tools.rst - expand_tooluniverse/reference/index.rst **list-table indentation** (3 files) Option lines and list items were indented with 1 space (only valid for 3-space) so Sphinx silently dropped them and reported "exactly one bullet list expected": - guide/finding_tools.rst - guide/http_api.rst - guide/tools.rst **Code-block separators** (5 files, ~30 directives) Add the required blank line between an introductory paragraph and a following ``.. code-block::``. Without it, Sphinx treated the directive as a continuation of the paragraph and emitted "Unexpected indentation" for every line of the code: - guide/literature_search_tools_tutorial.rst - expand_tooluniverse/quick_start.rst - expand_tooluniverse/contributing/local_tools.rst - expand_tooluniverse/contributing/remote_tools.rst - guide/make_your_data_agent_searchable.rst **Heading-style + indentation** (3 files) - guide/building_ai_scientists/mcp_name_shortening.rst — strip stray leading spaces from two section titles + downgrade unknown ``.. critical::`` to ``.. important::`` - about/deployment.rst — remove rogue ``=========`` underline below numbered-list items that mis-led the parser into skipping heading levels - guide/make_your_data_agent_searchable.rst — extend four "title underline too short" underlines + convert four markdown ``` fences to RST literal blocks **Misc directive / target fixes** - guide/python_guide.rst — replace nonexistent ``.. success::`` with a tip-styled ``.. admonition::`` - guide/euhealth_tools_tutorial.rst — indent ``.. note::`` body so it is no longer an empty admonition - help/troubleshooting.rst — same fix + remove rogue ``=========`` line that was being read as a section overline - tools/cellosaurus_tools.rst — wrap ``CVCL_`` in literal backticks so the trailing underscore stops triggering missing-target lookups - expand_tooluniverse/index.rst — promote two leading-space bullet lists to standalone lists so the indentation is correct - expand_tooluniverse/reference/architecture.rst — switch ``.. graphviz::`` (extension not installed) to a plain ``.. code-block:: text``; the embedded content was Mermaid pseudo-code anyway - guide/tools.rst — strip leading space on a section title * docs: clear all remaining content warnings (lists, headings, refs, grids) Round-4 build cleanup. Builds now finish with 0 structural ERRORs and 0 content WARNINGs; the only remaining ~11 warnings are pre-existing autodoc infrastructure noise (duplicate object index entries from autosummary, and the ghost_tool / medrxiv_tool modules that genuinely fail to import) — none are in hand-written documentation. Fixes in this commit: **sphinx-design grids** (python_guide.rst) Re-indent two ``.. grid::`` blocks whose first card + options used 1-space indentation (Sphinx silently dropped them → "parent of grid-item should be grid-row"). Also fix a ``.. button-ref::`` whose content was indented 1 space, producing a broken ``:any:`` cross-reference, and point it at the absolute ``/api/modules``. **Numbered/bulleted sub-lists** (tool_composition, literature_search ×2, architecture, literature_search_web_ui, make_your_data, agentic_tools, finding_tools, euhealth) Insert the required blank line before nested lists and re-indent 1-space sub-bullets to align under their parent list marker. Clears ~80 "list ends without a blank line; unexpected unindent" warnings. **Title underlines** (logging, tool_caller, loading_tools, tool_composition, euhealth, make_your_data, contributing/local_tools, reference/index, remote_tools/tutorial, troubleshooting + bulk pass) Extend underlines shorter than their title text; strip stray leading spaces from section titles that Sphinx read as block quotes. **Stray markdown in RST** (make_your_data, local_tools) Convert leftover ``###`` headings and ``` ``` fences to proper RST directives; remove a rogue ``------`` separator that was being parsed as a section underline. **Duplicate autosectionlabel** (make_your_data) Rename the second "How it works" heading to "How sharing works". **uniprot_tools** (JSON + generated RST) Rephrase the ``min_length`` / ``max_length`` descriptions so the open-ended range syntax no longer contains a bare ``*`` that RST read as an unterminated emphasis marker. Fixed in the JSON source so it survives doc regeneration.
ToolUniverse: Democratizing AI scientists
Install
AI agent (recommended) — open your AI agent and run:
Read https://aiscientist.tools/setup.md and set up ToolUniverse for me.
The agent will walk you through MCP configuration, API keys, skill installation, and validation.
or set up manually
Add to your MCP config file:
{
"mcpServers": {
"tooluniverse": {
"command": "uvx",
"args": ["--refresh", "tooluniverse"],
"env": {"PYTHONIOENCODING": "utf-8"}
}
}
}
Install agent skills:
npx skills add mims-harvard/ToolUniverse
Python developers — install the SDK:
uv pip install tooluniverse
tu CLI — discover, inspect, run, and test tools from the terminal.
Python SDK — programmatic access for building AI scientist systems.
Building AI Scientists with ToolUniverse
Click to watch the demo (YouTube) (Bilibili)
What is ToolUniverse?
ToolUniverse is an ecosystem for creating AI scientist systems from any large language model. Powered by the AI-Tool Interaction Protocol, it standardizes how LLMs identify and call tools, integrating more than 1000 machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design.
Key features:
- AI-Tool Interaction Protocol: Standardized interface governing how AI scientists issue tool requests and receive results
- Universal AI Model Support: Works with Claude, GPT, Gemini, Qwen, Deepseek, and open models
- MCP Integration: Native Model Context Protocol server with configurable transport and tool selection
- Async Operations: Long-running tasks (protein docking, molecular simulations) with progress tracking and parallel execution
- Tool Composition: Chain tools for sequential or parallel execution in self-directed workflows
- Compact Mode: Reduces 1000+ tools to 4-5 core discovery tools, saving ~99% context window
- CLI (
tu): Discover, inspect, run, and test tools directly from the terminal — 9 subcommands for interactive and scripted workflows - Agent Skills: 68 pre-built research workflows for drug discovery, precision oncology, rare disease diagnosis, pharmacovigilance, and more
- Literature Search: Unified search across PubMed, Semantic Scholar, ArXiv, BioRxiv, Europe PMC, and more
- Two-Tier Result Caching: In-memory LRU + SQLite persistence with per-tool fingerprinting for 10x speedup, offline support, and reproducibility
- Continuous Expansion: Register new tools locally or remotely without additional configuration
AI Scientists Powered by ToolUniverse
Building your project with ToolUniverse? Submit via GitHub Pull Request or contact us.
TxAgent: AI Agent for Therapeutic Reasoning [Project] [Paper] [PyPI] [GitHub] [HuggingFace]
TxAgent leverages ToolUniverse's scientific tool ecosystem to solve complex therapeutic reasoning tasks.
Medea: An Omics AI Agent for Therapeutic Discovery [Project] [Paper] [GitHub]
Medea integrates ToolUniverse tools for multi-omics analysis to identify therapeutic targets and predict drug responses across cancer, autoimmune, and other diseases.
Documentation
Full documentation: zitniklab.hms.harvard.edu/ToolUniverse
- CLI Reference (
tu) - Python Developer Guide
- AI Agent Setup
- Agent Skills
- Expand ToolUniverse
- API Reference
Community
Shanghua Gao, the lead creator of this project, is currently on the job market.
Slack · GitHub Issues · Shanghua Gao · Marinka Zitnik
Leaders: Shanghua Gao · Marinka Zitnik
Contributors: Shanghua Gao · Richard Zhu · Pengwei Sui · Zhenglun Kong · Sufian Aldogom · Yepeng Huang · Ayush Noori · Reza Shamji · Krishna Parvataneni · Theodoros Tsiligkaridis · Marinka Zitnik
Citation
@article{gao2025democratizingaiscientistsusing,
title={Democratizing AI scientists using ToolUniverse},
author={Shanghua Gao and Richard Zhu and Pengwei Sui and Zhenglun Kong and Sufian Aldogom and Yepeng Huang and Ayush Noori and Reza Shamji and Krishna Parvataneni and Theodoros Tsiligkaridis and Marinka Zitnik},
year={2025},
eprint={2509.23426},
archivePrefix={arXiv},
primaryClass={cs.AI},
url={https://arxiv.org/abs/2509.23426},
}