tooluniverse 1.0.1__tar.gz → 1.0.3__tar.gz

{tooluniverse-1.0.1/src/tooluniverse.egg-info → tooluniverse-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tooluniverse
-Version: 1.0.1
+Version: 1.0.3
 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
@@ -63,49 +63,82 @@ Provides-Extra: all
 Requires-Dist: tooluniverse[dev,docs,graph]; extra == "all"
 Dynamic: license-file
 
-# ToolUniverse
+# <img src="docs/_static/logo.png" alt="ToolUniverse Logo" height="28" style="vertical-align: middle; margin-right: 8px;" /> ToolUniverse: Democratizing AI scientists
 
-[![ToolUniverse-PIP](https://img.shields.io/badge/Pip-ToolUniverse-blue)](https://pypi.org/project/tooluniverse/)
+[![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)
+[![🌐Web Service](https://img.shields.io/badge/Web_Service-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)
 
-**Democratizing AI Scientists for Collaborative Discovery** 🌐 [Web Service](https://aiscientist.tools) | 📦 [PyPI](https://pypi.org/project/tooluniverse) | 📚 [Documentation](https://zitniklab.hms.harvard.edu/bioagent/)
 
 
+**Democratizing AI scientists using ToolUniverse**
+
 ToolUniverse is an ecosystem for creating AI scientist systems from any open or closed large language model (LLM). It standardizes how LLMs identify and call tools, integrating more than **600 machine learning models, datasets, APIs, and scientific packages** for data analysis, knowledge retrieval, and experimental design.
 
-## What is ToolUniverse?
+<div align="center">
+
+[![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)
+
+[![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>
+
+→ **Complete Tool List**: [Available Tools](https://zitniklab.hms.harvard.edu/bioagent/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
+
+
+## 🔬 What is ToolUniverse?
 
 AI scientists are emerging computational systems that serve as collaborative partners in discovery. However, these systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools, data, and analysts into a common ecosystem.
 
-ToolUniverse addresses this challenge by providing a standardized ecosystem that transforms any AI model into a powerful research scientist. By abstracting capabilities behind a unified interface, ToolUniverse wraps around any AI model (LLM, AI agent, or large reasoning model) and enables users to create and refine entirely custom AI research assistants without additional training or finetuning.
+ToolUniverse addresses this challenge by providing a standardized ecosystem that transforms any AI model into a powerful research scientist. By abstracting capabilities behind a unified interface, ToolUniverse wraps around any AI model (LLM, AI agent, or large reasoning model) and enables users to create and refine entirely custom AI scientists without additional training or finetuning.
 
 **Key Features:**
 
-- **AI-Tool Interaction Protocol**: Standardized interface governing how AI scientists issue tool requests and receive results
-- **Universal AI Model Support**: Works with any LLM, AI agent, or large reasoning model (GPT, Claude, Gemini, open models)
-- **Find Tool & Call Tool Operations**: Maps natural-language descriptions to tool specifications and executes tools with structured results
-- **Tool Composition & Workflows**: Chains tools for sequential or parallel execution in self-directed workflows
-- **Continuous Expansion**: New tools can be registered locally or remotely without additional configuration
+- [**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
+
+
+
 
 <!-- ![TxAgent](img/TxAgent_ToolUniverse.jpg) -->
 
 ## 🚀 Quick Start
 
-**Build your first AI scientist in 5 minutes:**
-
 ```python
 # 1. Install ToolUniverse
 pip install tooluniverse
 
-# 2. Create AI scientist system
+# 2. Load tooluniverse
 from tooluniverse import ToolUniverse
 
 tu = ToolUniverse()
 tu.load_tools()  # Load 600+ scientific tools
 
+# Your AI scientist can reason, experiment, and collaborate in discovery using the AI-tool interaction protocol.
+
 # 3. Use Find Tool operation to discover relevant tools
 tools = tu.run({
     "name": "Tool_Finder_Keyword",
@@ -115,48 +148,21 @@ tools = tu.run({
 # 4. Use Call Tool operation to execute selected tool
 result = tu.run({
     "name": "OpenTargets_get_associated_targets_by_disease_efoId",
-    "arguments": {"efoId": "EFO_0000249"}  # Alzheimer's disease
+    "arguments": {"efoId": "EFO_0000249"}
 })
 ```
 
-**Success!** Your AI scientist can now reason, experiment, and collaborate in discovery using the AI-tool interaction protocol.
-
-→ **Complete Quick Start Tutorial**: [Quick Start Tutorial](https://zitniklab.hms.harvard.edu/bioagent/quickstart.html)
+→ **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)
 
 
 ## 📦 Installation
 
-### Recommended Installation (uv)
+### Installation (uv)
 
 ```bash
-uv add tooluniverse
+uv pip install tooluniverse
 ```
 
-### Standard Installation (pip)
-
-```bash
-pip install tooluniverse
-```
-
-
-### Development Installation
-
-```bash
-git clone https://github.com/mims-harvard/ToolUniverse.git
-cd ToolUniverse
-uv sync  # or pip install -e .[dev]
-
-# Auto-setup pre-commit hooks
-./setup_precommit.sh
-```
-
-**Pre-commit Hooks:**
-Pre-commit hooks ensure code quality on every commit:
-- **Code formatting** with Black
-- **Linting** with flake8 and ruff
-- **Import cleanup** with autoflake
-- **File validation** (YAML, TOML, AST checks)
-
 → **Complete Installation Tutorial**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/bioagent/installation.html)
 
 ## 🔧 Usage & Integration
@@ -174,7 +180,7 @@ tu.load_tools()
 
 # Find relevant tools
 tools = tu.run({
-    "name": "Tool_Finder_Keyword",
+    "name": "Tool_Finder_Keyword", # Tool_Finder (Embedding model, GPU required), Tool_Finder_LLM (LLM-based model)
     "arguments": {"query": "protein structure prediction"}
 })
 
@@ -185,38 +191,60 @@ result = tu.run({
 })
 ```
 
-### AI Assistant Integration
+→ **Complete Tutorials**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/bioagent/installation.html)
 
-**🖥️ Claude Desktop**: Native integration with Claude AI assistant → [Setup Tutorial](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/claude_desktop.html)
-**💻 Claude Code**: Claude Code environment integration → [Setup Tutorial](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/claude_code.html)
-**🔮 Gemini CLI**: Google's AI agent integration → [Setup Tutorial](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/gemini_cli.html)
-**🧠 Qwen Code**: AI scientist integration with Qwen Code environment → [Setup Tutorial](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/qwen_code.html)
-**⚡ GPT Codex CLI**: Terminal-based AI scientist with Codex CLI → [Setup Tutorial](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/codex_cli.html)
-**🎯 ChatGPT API**: OpenAI integration via MCP protocol and function calling → [Setup Tutorial](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/chatgpt_api.html)
+### MCP Support
 
-→ **AI Assistant Setup Guides**: [Building AI Scientists](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/index.html)
+```python
+# 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)
 
-### MCP Server Integration
 
-```bash
-# Start MCP server
-python -m tooluniverse.smcp_server
+## 🚀 AI Scientists Projects Powered by ToolUniverse
 
-# Or with CLI
-tooluniverse-mcp --help
-```
+*Building your own project with ToolUniverse? We'd love to feature it here! Submit your project via [GitHub Pull Request](https://github.com/mims-harvard/ToolUniverse/pulls) or contact us.*
 
-### Core Capabilities
+---
+**TxAgent: AI Agent for Therapeutic Reasoning** [[Project]](https://zitniklab.hms.harvard.edu/TxAgent) [[Paper]](https://arxiv.org/pdf/2503.10970) [[PiPy]](https://pypi.org/project/txagent/) [[Github]](https://github.com/mims-harvard/TxAgent) [[HuggingFace]](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
+> **TxAgent** is an AI agent for therapeutic reasoning that leverages ToolUniverse's comprehensive scientific tool ecosystem to solve complex therapeutic reasoning tasks. 
 
-- **🔍 Find Tool Operation**: Maps natural-language descriptions to tool specifications using semantic search
-- **⚙️ Call Tool Operation**: Executes selected tools with structured arguments and returns text, embeddings, or JSON
-- **🔗 Tool Composition**: Chains tools for sequential or parallel execution in self-directed workflows
-- **🛠️ Tool Creation**: Automatically creates new tools from natural language descriptions
-- **🔄 Iterative Optimization**: Refines tool interfaces and specifications for correct use by AI scientists
-- **🌐 Shared Environment**: Unifies tools, data, and analysts into a common ecosystem for interoperability and reuse
 
-→ **Detailed Usage Tutorial**: [README_USAGE.md](README_USAGE.md)
-→ **Complete Getting Started**: [Getting Started Tutorial](https://zitniklab.hms.harvard.edu/bioagent/getting_started.html)
+---
+**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)
+
+---
+
+
+## 🤝 Contribution and Community
+
+**We are actively looking for core contributors for ToolUniverse!**
+Please join our [Slack Channel](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ) or reach out to [Shanghua Gao](mailto:shanghuagao@gmail.com)/[Marinka Zitnik](mailto:marinka@hms.harvard.edu).
+
+**Get Involved:**
+
+- **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)
+
+
+
+### Contributors
+
+- **[Shanghua Gao](https://shgao.site)**
+- **[Richard Zhu](https://www.linkedin.com/in/richard-zhu-4236901a7/)**
+- **[Pengwei Sui](mailto:pengwei_sui@hms.harvard.edu)**
+- **[Zhenglun Kong](https://zlkong.github.io/homepage/)**
+- **[Sufian Aldogom](mailto:saldogom@mit.edu)**
+- **[Yepeng Huang](mailto:yepeng_huang@hms.harvard.edu)**
+- **[Ayush Noori](https://www.ayushnoori.com/)**
+- **[Reza Shamji](mailto:reza_shamji@hms.harvard.edu)**
+- **[Krishna Parvataneni](mailto:krishna_parvataneni@hms.harvard.edu)**
+- **[Theodoros Tsiligkaridis](https://sites.google.com/view/theo-t)**
+- **[Marinka Zitnik](https://zitniklab.hms.harvard.edu/)**
+
 
 
 ## 📚 Documentation
@@ -235,108 +263,39 @@ Our comprehensive documentation covers everything from quick start to advanced w
 - **[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
-
-### 🤖 Building AI Scientists
-- **[Overview](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/index.html)**: Create AI research assistants 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
+- **[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
 
 ### 🛠️ 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
 
 ### 🔧 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 Tutorial
+- **[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
 
 ### 📚 API Reference
-- **[API Directory](https://zitniklab.hms.harvard.edu/bioagent/api_directory.html)**: Complete tool listing
-- **[Tools Reference](https://zitniklab.hms.harvard.edu/bioagent/api/tools_complete_reference.html)**: Detailed API documentation
-- **[Quick Reference](https://zitniklab.hms.harvard.edu/bioagent/api_quick_reference.html)**: Essential API Tutorial
-
-### 🆘 Help & Support
-- **[FAQ](https://zitniklab.hms.harvard.edu/bioagent/faq.html)**: Frequently asked questions
-- **[Troubleshooting](https://zitniklab.hms.harvard.edu/bioagent/troubleshooting.html)**: Common issues and solutions
-- **[Help Index](https://zitniklab.hms.harvard.edu/bioagent/help/index.html)**: Support resources
+- **[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
 
 → **Browse All Documentation**: [ToolUniverse Documentation](https://zitniklab.hms.harvard.edu/bioagent/)
 
-## 🚀 AI Scientists Projects Powered by ToolUniverse
-
-### TxAgent: AI Agent for Therapeutic Reasoning
-
-**TxAgent** is an AI agent for therapeutic reasoning that leverages ToolUniverse's comprehensive scientific tool ecosystem to solve complex therapeutic reasoning tasks.
-
-[![ProjectPage](https://img.shields.io/badge/Page-TxAgent-red)](https://zitniklab.hms.harvard.edu/TxAgent) [![PaperLink](https://img.shields.io/badge/Arxiv-TxAgent-red)](https://arxiv.org/pdf/2503.10970) [![TxAgent-PIP](https://img.shields.io/badge/Pip-TxAgent-blue)](https://pypi.org/project/txagent/) [![TxAgent](https://img.shields.io/badge/Code-TxAgent-purple)](https://github.com/mims-harvard/TxAgent) [![HuggingFace](https://img.shields.io/badge/HuggingFace-TxAgentT1-yellow)](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
-
----
-
-*Building your own project with ToolUniverse? We'd love to feature it here! Submit your project via [GitHub Issues](https://github.com/mims-harvard/ToolUniverse/issues) or contact us.*
-
-## 🌍 Ecosystem & Community
-
-### Democratizing AI Agents for Science
-
-ToolUniverse addresses the fundamental challenge that AI scientists remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments. Drawing inspiration from how unified ecosystems have transformed omics research by enabling interoperability, reuse, and community-driven development, ToolUniverse provides comparable infrastructure for AI scientists.
-
-**Core Principles:**
-
-- **🔓 Unified Ecosystem**: Integrates tools, data, and analysts into a common environment like omics platforms
-- **📐 Standardized Protocol**: AI-tool interaction protocol analogous to HTTP for internet communication
-- **🔗 Interoperability**: Tool specification schema that standardizes definitions and enables consistent inference
-- **🌐 Collaborative Discovery**: Enables AI scientists to serve as computational partners in research
-- **🚀 Scalable Construction**: Builds AI scientists at scale without bespoke implementation
 
-### Research Applications
-
-**🧬 Drug Discovery & Development**
-- Target identification and validation
-- Compound screening and optimization
-- Safety and toxicity assessment
-- Clinical trial analysis and outcomes
-- **Case Study**: Hypercholesterolemia research where ToolUniverse enabled an AI scientist to identify a potent drug analog with favorable predicted properties
-
-**🔬 Molecular Biology Research**
-- Gene function annotation and analysis
-- Protein structure prediction and modeling
-- Pathway analysis and network construction
-- Disease association studies
-
-**📊 Literature & Knowledge Mining**
-- Automated systematic literature reviews
-- Named entity recognition and extraction
-- Citation network analysis and mapping
-- Patent landscape analysis and IP research
-
-**🤖 AI-Driven Research Automation**
-- Hypothesis generation and testing
-- Experimental design optimization
-- Multi-modal data analysis and integration
-- Results interpretation and reporting
-
-### Community & Support
-
-**Get Involved:**
-- 🐛 **Report Issues**: [GitHub Issues](https://github.com/mims-harvard/ToolUniverse/issues)
-- 💬 **Join Discussions**: [GitHub Discussions](https://github.com/mims-harvard/ToolUniverse/discussions)
-- 📧 **Contact**: Visit [aiscientist.tools](https://aiscientist.tools) for more information
-- 🤝 **Contribute**: See our [Contributing Tutorial](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/comprehensive_tool_guide.html)
-
-**Integrations & Extensions:**
-- **Model Context Protocol (MCP)**: Full MCP server support for AI assistant integration
-- **Claude Desktop**: Native integration with Anthropic's Claude Desktop App
-- **OpenAI Function Calling**: Direct integration with ChatGPT and GPT models
-- **Custom Agents**: Build domain-specific AI research assistants
-
-## Citation
+### Citation
 
 ```
 @misc{gao2025txagent,
@@ -350,31 +309,6 @@ ToolUniverse addresses the fundamental challenge that AI scientists remain diffi
 }
 ```
 
-##  Contact & Contributors
-
-### Contact
-
-For questions, suggestions, or collaboration opportunities:
-
-- **📧 Contact**: [Shanghua Gao](mailto:shanghuagao@gmail.com)
-- **🌐 Web Platform**: [aiscientist.tools](https://aiscientist.tools)
-- **💻 GitHub**: [github.com/mims-harvard/ToolUniverse](https://github.com/mims-harvard/ToolUniverse)
-
-### Contributors
-
-- **[Shanghua Gao](https://shgao.site)**
-- **[Richard Zhu](https://www.linkedin.com/in/richard-zhu-4236901a7/)**
-- **[Pengwei Sui](mailto:pengwei_sui@hms.harvard.edu)**
-- **[Zhenglun Kong](https://zlkong.github.io/homepage/)**
-- **[Sufian Aldogom](mailto:saldogom@mit.edu)**
-- **[Yepeng Huang](mailto:yepeng_huang@hms.harvard.edu)**
-- **[Ayush Noori](https://www.ayushnoori.com/)**
-- **[Reza Shamji](mailto:reza_shamji@hms.harvard.edu)**
-- **[Krishna Parvataneni](mailto:krishna_parvataneni@hms.harvard.edu)**
-- **[Theodoros Tsiligkaridis](https://sites.google.com/view/theo-t)**
-- **[Marinka Zitnik](https://zitniklab.hms.harvard.edu/)**
-
-
 
 ### Acknowledgments
 
@@ -382,6 +316,4 @@ ToolUniverse is developed by the [Zitnik Lab](https://zitniklab.hms.harvard.edu/
 
 ---
 
-**🧬🤖🔬 Happy researching with ToolUniverse!**
-
-*Democratizing AI agents for science - one tool at a time.*
+*Democratizing AI agents for science with ToolUniverse.*