tooluniverse 1.0.4__tar.gz → 1.0.6__tar.gz

tooluniverse-1.0.6/LICENSE

@@ -0,0 +1,201 @@
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+   Copyright [2025] [ToolUniverse team]
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{tooluniverse-1.0.4/src/tooluniverse.egg-info → tooluniverse-1.0.6}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: tooluniverse
-Version: 1.0.4
+Version: 1.0.6
 Summary: A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows.
 Author-email: Shanghua Gao <shanghuagao@gmail.com>
-Project-URL: Homepage, https://github.com/mims-harvard/TxAgent
+Project-URL: Homepage, https://github.com/mims-harvard/ToolUniverse
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
@@ -38,19 +38,29 @@ Requires-Dist: aiohttp
 Provides-Extra: dev
 Requires-Dist: pytest>=6.0; extra == "dev"
 Requires-Dist: pytest-cov>=2.0; extra == "dev"
+Requires-Dist: pytest-timeout>=2.3.1; extra == "dev"
+Requires-Dist: pytest-mock>=3.14.0; extra == "dev"
+Requires-Dist: requests-mock>=1.12.1; extra == "dev"
 Requires-Dist: black>=22.0; extra == "dev"
 Requires-Dist: flake8>=4.0; extra == "dev"
 Requires-Dist: pre-commit>=2.0; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: sphinx>=4.0; extra == "docs"
+Requires-Dist: furo>=2024.8.6; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.15.0; extra == "docs"
 Requires-Dist: sphinx-rtd-theme>=1.0; extra == "docs"
 Requires-Dist: myst-parser>=0.18; extra == "docs"
+Requires-Dist: linkify-it-py>=2.0.0; extra == "docs"
 Requires-Dist: sphinx-autobuild>=2021.3.14; extra == "docs"
 Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
 Requires-Dist: sphinx-tabs>=3.2.0; extra == "docs"
 Requires-Dist: sphinx-design>=0.3.0; extra == "docs"
 Requires-Dist: sphinx-notfound-page>=0.8; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints>=1.12.0; extra == "docs"
+Provides-Extra: embedding
+Requires-Dist: sentence-transformers>=5.1.0; extra == "embedding"
+Requires-Dist: faiss-cpu>=1.12.0; extra == "embedding"
+Requires-Dist: huggingface_hub>=0.34.0; extra == "embedding"
 Provides-Extra: graph
 Requires-Dist: flask>=2.0.0; extra == "graph"
 Requires-Dist: matplotlib>=3.5.0; extra == "graph"
@@ -66,11 +76,12 @@ Dynamic: license-file
 
 # <img src="docs/_static/logo.png" alt="ToolUniverse Logo" height="28" style="vertical-align: middle; margin-right: 8px;" /> ToolUniverse: Democratizing AI scientists
 
+[![Paper](https://img.shields.io/badge/Paper-Arxiv-blue)](https://arxiv.org/abs/2509.23426)
 [![ToolUniverse-PIP](https://img.shields.io/badge/PyPI-ToolUniverse-blue)](https://pypi.org/project/tooluniverse/)
 [![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
 [![Model context protocol (MCP)](https://img.shields.io/badge/Model_Context_Protocol_(MCP)_Supported-green)](README_USAGE.md#running-the-mcp-server)
-[![Documentation](https://img.shields.io/badge/Documentation-Available-green)](https://zitniklab.hms.harvard.edu/bioagent/)
-[![🌐Web Service](https://img.shields.io/badge/Web_Service-aiscientist.tools-blue)](https://aiscientist.tools)
+[![Documentation](https://img.shields.io/badge/Documentation-Available-green)](https://zitniklab.hms.harvard.edu/ToolUniverse/)
+[![🌐Web](https://img.shields.io/badge/Website-aiscientist.tools-blue)](https://aiscientist.tools)
 [![Slack](https://img.shields.io/badge/Slack-Join_Community-orange)](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ)
 
 
@@ -84,27 +95,34 @@ ToolUniverse is an ecosystem for creating AI scientist systems from any open or
 [![Visit Website](https://img.shields.io/badge/Visit_Website-AIScientist.Tools-4285F4?style=for-the-badge&logo=google-chrome&logoColor=white)](https://aiscientist.tools)
 
 [![Join Slack Community](https://img.shields.io/badge/Join_Slack_Community-Get_Help_&_Connect-FF6B6B?style=for-the-badge&logo=slack&logoColor=white)](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ)
-[![Join WeChat Group](https://img.shields.io/badge/Join_WeChat_Group-Community_&_Discussion-07C160?style=for-the-badge&logo=wechat&logoColor=white)](https://zitniklab.hms.harvard.edu/bioagent/wechat_community.html)
+[![Join WeChat Group](https://img.shields.io/badge/Join_WeChat_Group-Community_&_Discussion-07C160?style=for-the-badge&logo=wechat&logoColor=white)](https://aiscientist.tools/wechat)
 
 [![Follow on LinkedIn](https://img.shields.io/badge/Follow_on_LinkedIn-Professional_Updates-0077B5?style=for-the-badge&logo=linkedin&logoColor=white)](https://www.linkedin.com/in/tooluniverse-at-harvard-b9aa88385/)
 [![Follow on X](https://img.shields.io/badge/Follow_on_X-Latest_Updates-000000?style=for-the-badge&logo=x&logoColor=white)](https://x.com/ScientistTools)
 
 </div>
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/13ddb54c-4fcc-4507-8695-1c58e7bc1e68" width="600" />
+</p>
 
-→ **Complete Tool List**: [Available Tools](https://zitniklab.hms.harvard.edu/bioagent/tools/tools_config_index.html)
+→ **Complete Tool List**: [Available Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/tools/tools_config_index.html)
 
 → **Check our website for direct tool usage**: [AIScientist.Tools](https://aiscientist.tools/)
 
 
 ## 🤖 Building AI Scientists with ToolUniverse in 5 minutes
-- **[Overview](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/index.html)**: Create AI scientists from any LLM
-- **[Claude Desktop Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/claude_desktop.html)**: Native MCP integration with Claude Desktop App
-- **[Claude Code Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/claude_code.html)**: AI scientist development in Claude Code environment
-- **[Gemini CLI Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/gemini_cli.html)**: Command-line scientific research with Google Gemini
-- **[Qwen Code Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/qwen_code.html)**: AI scientist workflows in Qwen Code environment
-- **[GPT Codex CLI Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/codex_cli.html)**: Terminal-based research with OpenAI Codex
-- **[ChatGPT API Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/chatgpt_api.html)**: Programmatic research with ChatGPT function calling
 
+[![YouTube Video](https://img.youtube.com/vi/fManSJlSs60/maxresdefault.jpg)](https://www.youtube.com/watch?v=fManSJlSs60)
+*Click the image above to watch the ToolUniverse demonstration*
+[(Also in Bilibili)](https://www.bilibili.com/video/BV1GynhzjEos/?share_source=copy_web&vd_source=b398f13447281e748f5c41057a2c6858)
+
+- **[Overview](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/index.html)**: Create AI scientists from any LLM
+- **[Claude Desktop Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/claude_desktop.html)**: Native MCP integration with Claude Desktop App
+- **[Claude Code Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/claude_code.html)**: AI scientist development in Claude Code environment
+- **[Gemini CLI Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/gemini_cli.html)**: Command-line scientific research with Google Gemini
+- **[Qwen Code Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/qwen_code.html)**: AI scientist workflows in Qwen Code environment
+- **[GPT Codex CLI Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/codex_cli.html)**: Terminal-based research with OpenAI Codex
+- **[ChatGPT API Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/chatgpt_api.html)**: Programmatic research with ChatGPT function calling
 
 ## 🔬 What is ToolUniverse?
 
@@ -114,18 +132,19 @@ ToolUniverse addresses this challenge by providing a standardized ecosystem that
 
 **Key Features:**
 
-- [**AI-Tool Interaction Protocol**](https://zitniklab.hms.harvard.edu/bioagent/guide/interaction_protocol.html): Standardized interface governing how AI scientists issue tool requests and receive results
-- [**Universal AI Model Support**](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/index.html): Works with any LLM, AI agent, or large reasoning model (GPT5, Claude, Gemini, Qwen, Deepseek, open models)
-- [**Easy to Load & Find & Call Tool**](https://zitniklab.hms.harvard.edu/bioagent/guide/index.html) (*[WebService](https://aiscientist.tools/), [PythonAPI](https://zitniklab.hms.harvard.edu/bioagent/api/modules.html), [MCP](https://zitniklab.hms.harvard.edu/bioagent/guide/mcp_support.html)*): Maps natural-language descriptions to tool specifications and executes tools with structured results 
-- [**Tool Composition & Scientific Workflows**](https://zitniklab.hms.harvard.edu/bioagent/guide/tool_composition.html): Chains tools for sequential or parallel execution in self-directed scientific workflows
-- [**Continuous Expansion**](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/index.html): New tools can be easily registered locally or remotely without additional configuration
-- [**Multi-Agent Tool Creation & Optimization**](https://zitniklab.hms.harvard.edu/bioagent/guide/scientific_workflows.html): Multi-agent powered tool construction and iterative tool optimization
-
+- [**AI-Tool Interaction Protocol**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/interaction_protocol.html): Standardized interface governing how AI scientists issue tool requests and receive results
+- [**Universal AI Model Support**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/index.html): Works with any LLM, AI agent, or large reasoning model (GPT5, Claude, Gemini, Qwen, Deepseek, open models)
+- [**OpenRouter Integration**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/openrouter_support.html): Access 100+ models from OpenAI, Anthropic, Google, Qwen, and more through a single API
+- [**Easy to Load & Find & Call Tool**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/index.html) (*[WebService](https://aiscientist.tools/), [PythonAPI](https://zitniklab.hms.harvard.edu/ToolUniverse/api/modules.html), [MCP](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/mcp_support.html)*): Maps natural-language descriptions to tool specifications and executes tools with structured results 
+- [**Tool Composition & Scientific Workflows**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tool_composition.html): Chains tools for sequential or parallel execution in self-directed scientific workflows
+- [**Continuous Expansion**](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/index.html): New tools can be easily registered locally or remotely without additional configuration
+- [**Multi-Agent Tool Creation & Optimization**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/scientific_workflows.html): Multi-agent powered tool construction and iterative tool optimization
 
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/eb15bd7c-4e73-464b-8d65-733877c96a51" width="888" />
+</p>
 
 
-<!-- ![TxAgent](img/TxAgent_ToolUniverse.jpg) -->
-
 ## 🚀 Quick Start
 
 ```python
@@ -143,17 +162,17 @@ tu.load_tools()  # Load 600+ scientific tools
 # 3. Use Find Tool operation to discover relevant tools
 tools = tu.run({
     "name": "Tool_Finder_Keyword",
-    "arguments": {"query": "disease target associations"}
+    "arguments": {"description": "disease target associations", "limit": 10}
 })
 
 # 4. Use Call Tool operation to execute selected tool
 result = tu.run({
     "name": "OpenTargets_get_associated_targets_by_disease_efoId",
-    "arguments": {"efoId": "EFO_0000249"}
+    "arguments": {"efoId": "EFO_0000537"}  # hypertension
 })
 ```
 
-→ **Complete Quick Start Tutorial**: [Quick Start Tutorial](https://zitniklab.hms.harvard.edu/bioagent/quickstart.html) [Getting Started Tutorial](https://zitniklab.hms.harvard.edu/bioagent/getting_started.html)
+→ **Complete Quick Start Tutorial**: [Quick Start Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/quickstart.html) [Getting Started Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/getting_started.html)
 
 
 ## 📦 Installation
@@ -164,7 +183,7 @@ result = tu.run({
 uv pip install tooluniverse
 ```
 
-→ **Complete Installation Tutorial**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/bioagent/installation.html)
+→ **Complete Installation Tutorial**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/installation.html)
 
 ## 🔧 Usage & Integration
 
@@ -182,17 +201,18 @@ tu.load_tools()
 # Find relevant tools
 tools = tu.run({
     "name": "Tool_Finder_Keyword", # Tool_Finder (Embedding model, GPU required), Tool_Finder_LLM (LLM-based model)
-    "arguments": {"query": "protein structure prediction"}
+    "arguments": {"description": "protein structure prediction", "limit": 10}
 })
 
 # Execute tools
 result = tu.run({
-    "name": "UniProt_get_protein_info",
-    "arguments": {"gene_symbol": "BRCA1"}
+    "name": "UniProt_get_function_by_accession",
+    "arguments": {"accession": "P05067"}
 })
+
 ```
 
-→ **Complete Tutorials**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/bioagent/installation.html)
+→ **Complete Tutorials**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/installation.html)
 
 ### MCP Support
 
@@ -200,7 +220,7 @@ result = tu.run({
 # run one command to launch the tooluniverse mcp server
 tooluniverse-smcp
 ```
-→ **Complete Tutorial**: [MCP Support](https://zitniklab.hms.harvard.edu/bioagent/guide/mcp_support.html)
+→ **Complete Tutorial**: [MCP Support](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/mcp_support.html)
 
 
 ## 🚀 AI Scientists Projects Powered by ToolUniverse
@@ -213,9 +233,11 @@ tooluniverse-smcp
 
 
 ---
-**Hypercholesterolemia Drug Discovery** [[Tutorial]](https://zitniklab.hms.harvard.edu/bioagent/tutorials/tooluniverse_case_study.html) [[Code]](https://colab.research.google.com/drive/1UwJ6RwyUoqI5risKQ365EeFdDQWOeOCv?usp=sharing)
+**Hypercholesterolemia Drug Discovery** [[Tutorial]](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/tooluniverse_case_study.html) [[Code]](https://colab.research.google.com/drive/1UwJ6RwyUoqI5risKQ365EeFdDQWOeOCv?usp=sharing)
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/cc53e9b0-94d3-407d-a015-71762ddb9836" width="600" />
+</p>
 
----
 
 
 ## 🤝 Contribution and Community
@@ -228,7 +250,7 @@ Please join our [Slack Channel](https://join.slack.com/t/tooluniversehq/shared_i
 - **Report Issues**: [GitHub Issues](https://github.com/mims-harvard/ToolUniverse/issues)
 - **Join Discussions**: [Slack Channel](https://github.com/mims-harvard/ToolUniverse/discussions)
 - **Contact**: Reach out to [Shanghua Gao](shanghuagao@gmail.com)/[Marinka Zitnik](marinka@hms.harvard.edu)
-- **Contribute**: See our [Contributing Tutorial](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/comprehensive_tool_guide.html)
+- **Contribute**: See our [Contributing Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/comprehensive_tool_guide.html)
 
 
 
@@ -236,10 +258,10 @@ Please join our [Slack Channel](https://join.slack.com/t/tooluniversehq/shared_i
 
 - **[Shanghua Gao](https://shgao.site)**
 - **[Richard Zhu](https://www.linkedin.com/in/richard-zhu-4236901a7/)**
-- **[Pengwei Sui](mailto:pengwei_sui@hms.harvard.edu)**
+- **[Pengwei Sui](https://psui3905.github.io/)**
 - **[Zhenglun Kong](https://zlkong.github.io/homepage/)**
 - **[Sufian Aldogom](mailto:saldogom@mit.edu)**
-- **[Yepeng Huang](mailto:yepeng_huang@hms.harvard.edu)**
+- **[Yepeng Huang](https://yepeng.notion.site/Yepeng-Huang-16ad8dd1740080c28d4bd3e3d7c1080c)**
 - **[Ayush Noori](https://www.ayushnoori.com/)**
 - **[Reza Shamji](mailto:reza_shamji@hms.harvard.edu)**
 - **[Krishna Parvataneni](mailto:krishna_parvataneni@hms.harvard.edu)**
@@ -253,53 +275,63 @@ Please join our [Slack Channel](https://join.slack.com/t/tooluniversehq/shared_i
 Our comprehensive documentation covers everything from quick start to advanced workflows:
 
 ### 🚀 Getting Started
-- **[Quick Start Tutorial](https://zitniklab.hms.harvard.edu/bioagent/quickstart.html)**: 5-minute setup and first query
-- **[Installation](https://zitniklab.hms.harvard.edu/bioagent/installation.html)**: Complete installation options
-- **[Getting Started](https://zitniklab.hms.harvard.edu/bioagent/getting_started.html)**: Step-by-step tutorial
-- **[AI-Tool Protocol](https://zitniklab.hms.harvard.edu/bioagent/guide/interaction_protocol.html)**: Understanding the interaction protocol
+- **[Quick Start Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/quickstart.html)**: 5-minute setup and first query
+- **[Installation](https://zitniklab.hms.harvard.edu/ToolUniverse/installation.html)**: Complete installation options
+- **[Getting Started](https://zitniklab.hms.harvard.edu/ToolUniverse/getting_started.html)**: Step-by-step tutorial
+- **[AI-Tool Protocol](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/interaction_protocol.html)**: Understanding the interaction protocol
 
 ### 📖 User Guides
-- **[Loading Tools](https://zitniklab.hms.harvard.edu/bioagent/guide/loading_tools.html)**: Complete Tutorial to loading tools
-- **[Tool Discovery](https://zitniklab.hms.harvard.edu/bioagent/tutorials/finding_tools.html)**: Find tools by keyword, LLM, and embedding search
-- **[Tool Caller](https://zitniklab.hms.harvard.edu/bioagent/guide/tool_caller.html)**: Primary execution engine
-- **[Tool Composition](https://zitniklab.hms.harvard.edu/bioagent/guide/tool_composition.html)**: Chain tools into workflows
-- **[Scientific Workflows](https://zitniklab.hms.harvard.edu/bioagent/guide/scientific_workflows.html)**: Real-world research scenarios
-- **[MCP Support](https://zitniklab.hms.harvard.edu/bioagent/guide/mcp_support.html)**: Model Context Protocol integration
-- **[Logging](https://zitniklab.hms.harvard.edu/bioagent/guide/logging.html)**: Comprehensive logging configuration
+- **[Loading Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/loading_tools.html)**: Complete Tutorial to loading tools
+- **[Tool Discovery](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/finding_tools.html)**: Find tools by keyword, LLM, and embedding search
+- **[Tool Caller](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tool_caller.html)**: Primary execution engine
+- **[Tool Composition](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tool_composition.html)**: Chain tools into workflows
+- **[Scientific Workflows](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/scientific_workflows.html)**: Real-world research scenarios
+- **[MCP Support](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/mcp_support.html)**: Model Context Protocol integration
+- **[Logging](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/logging.html)**: Comprehensive logging configuration
 
 ### 🛠️ Advanced Features
-- **[Hooks System](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/index.html)**: Intelligent output processing
-  - **[Hook Configuration](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/hook_configuration.html)**: Configure hooks for different outputs
-  - **[File Save Hook](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/file_save_hook.html)**: Save tool outputs to files
-  - **[Summarization Hook](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/summarization_hook.html)**: Summarize tool outputs
-  - **[Server Stdio Hooks](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/server_stdio_hooks.html)**: Server communication hooks
-- **[Expert Feedback](https://zitniklab.hms.harvard.edu/bioagent/tutorials/expert_feedback.html)**: Human-in-the-loop consultation
-- **[Agentic Tools](https://zitniklab.hms.harvard.edu/bioagent/tutorials/agentic_tools_tutorial.html)**: AI-powered tool development
-- **[Case Study](https://zitniklab.hms.harvard.edu/bioagent/tutorials/tooluniverse_case_study.html)**: End-to-end drug discovery workflow
-- **[Tool Optimization](https://zitniklab.hms.harvard.edu/bioagent/tutorials/optimization/Tool_Description_Optimizer_Tutorial.html)**: Optimize tool descriptions for better performance
+- **[Hooks System](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/index.html)**: Intelligent output processing
+  - **[Hook Configuration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/hook_configuration.html)**: Configure hooks for different outputs
+  - **[File Save Hook](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/file_save_hook.html)**: Save tool outputs to files
+  - **[Summarization Hook](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/summarization_hook.html)**: Summarize tool outputs
+  - **[Server Stdio Hooks](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/server_stdio_hooks.html)**: Server communication hooks
+- **[Expert Feedback](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/expert_feedback.html)**: Human-in-the-loop consultation
+- **[Agentic Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/agentic_tools_tutorial.html)**: AI-powered tool development
+- **[Case Study](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/tooluniverse_case_study.html)**: End-to-end drug discovery workflow
+- **[Tool Optimization](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/optimization/Tool_Description_Optimizer_Tutorial.html)**: Optimize tool descriptions for better performance
 
 ### 🔧 Expanding ToolUniverse
-- **[Architecture](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/architecture.html)**: System architecture overview
-- **[Local Tool Registration](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/local_tool_registration.html)**: Create custom tools
-- **[Remote Tool Registration](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/remote_tool_registration.html)**: Integrate external services
-- **[Contributing Tools](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/comprehensive_tool_guide.html)**: Complete contribution guide
-- **[Adding Tools Tutorial](https://zitniklab.hms.harvard.edu/bioagent/tutorials/addtools/Adding_Tools_Tutorial.html)**: Step-by-step tool addition guide
-- **[MCP Tool Registration](https://zitniklab.hms.harvard.edu/bioagent/tutorials/addtools/mcp_tool_registration_en.html)**: Register tools via MCP
+- **[Architecture](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/architecture.html)**: System architecture overview
+- **[Local Tool Registration](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/local_tool_registration.html)**: Create custom tools
+- **[Remote Tool Registration](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/remote_tool_registration.html)**: Integrate external services
+- **[Contributing Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/comprehensive_tool_guide.html)**: Complete contribution guide
+- **[Adding Tools Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/addtools/Adding_Tools_Tutorial.html)**: Step-by-step tool addition guide
+- **[MCP Tool Registration](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/addtools/mcp_tool_registration_en.html)**: Register tools via MCP
 
 ### 📚 API Reference
-- **[API Directory](https://zitniklab.hms.harvard.edu/bioagent/api/modules.html)**: Complete module listing
-- **[Core Modules](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.html)**: Main ToolUniverse class and utilities
-- **[Tool Classes](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.base_tool.html)**: Base tool classes and implementations
-- **[Compose Scripts](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.compose_scripts.html)**: Tool composition utilities
-- **[MCP Integration](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.mcp_integration.html)**: Model Context Protocol support
+- **[API Directory](https://zitniklab.hms.harvard.edu/ToolUniverse/api/modules.html)**: Complete module listing
+- **[Core Modules](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.html)**: Main ToolUniverse class and utilities
+- **[Tool Classes](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.base_tool.html)**: Base tool classes and implementations
+- **[Compose Scripts](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.compose_scripts.html)**: Tool composition utilities
+- **[MCP Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.mcp_integration.html)**: Model Context Protocol support
 
-→ **Browse All Documentation**: [ToolUniverse Documentation](https://zitniklab.hms.harvard.edu/bioagent/)
+→ **Browse All Documentation**: [ToolUniverse Documentation](https://zitniklab.hms.harvard.edu/ToolUniverse/)
 
 
 ### Citation
 
 ```
-@misc{gao2025txagent,
+@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}, 
+}
+
+@article{gao2025txagent,
       title={TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools},
       author={Shanghua Gao and Richard Zhu and Zhenglun Kong and Ayush Noori and Xiaorui Su and Curtis Ginder and Theodoros Tsiligkaridis and Marinka Zitnik},
       year={2025},
@@ -310,11 +342,6 @@ Our comprehensive documentation covers everything from quick start to advanced w
 }
 ```
 
-
-### Acknowledgments
-
-ToolUniverse is developed by the [Zitnik Lab](https://zitniklab.hms.harvard.edu/) at Harvard Medical School in collaboration with MIT Lincoln Laboratory. We thank the scientific community for their valuable feedback and contributions.
-
 ---
 
 *Democratizing AI agents for science with ToolUniverse.*