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Merge branch 'main' into add-open-source-acknowledgements
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Haoxuan "Orion" Li
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README.md
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README.md
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# Claude Scientific Skills
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[](LICENSE.md)
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[](#whats-included)
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[](#whats-included)
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A comprehensive collection of **139 ready-to-use scientific skills** for Claude, created by [K-Dense](https://k-dense.ai). Transform Claude into your AI research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
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A comprehensive collection of **140 ready-to-use scientific skills** for Claude, created by [K-Dense](https://k-dense.ai). Transform Claude into your AI research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
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**Looking for the full AI co-scientist experience?** Try [K-Dense Web](https://app.k-dense.ai) for 200+ skills, cloud compute, and publication-ready outputs.
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**Looking for the full AI co-scientist experience?** Try [K-Dense Web](https://k-dense.ai) for 200+ skills, cloud compute, and publication-ready outputs.
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<p align="center">
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<a href="https://app.k-dense.ai">
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<a href="https://k-dense.ai">
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<img src="docs/k-dense-web.gif" alt="K-Dense Web Demo" width="800"/>
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</a>
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</p>
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## K-Dense Web - The Full Experience
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Want 10x the power with zero setup? **[K-Dense Web](https://app.k-dense.ai)** is the complete AI co-scientist platform—everything in this repo, plus:
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Want 10x the power with zero setup? **[K-Dense Web](https://k-dense.ai)** is the complete AI co-scientist platform—everything in this repo, plus:
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| Feature | This Repo | K-Dense Web |
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|---------|-----------|-------------|
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| Scientific Skills | 139 skills | **200+ skills** (exclusive access) |
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| Scientific Skills | 140 skills | **200+ skills** (exclusive access) |
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| Setup Required | Manual installation | **Zero setup** — works instantly |
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| Compute | Your machine | **Cloud GPUs & HPC** included |
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| Workflows | Basic prompts | **End-to-end research pipelines** |
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@@ -32,9 +32,9 @@ Want 10x the power with zero setup? **[K-Dense Web](https://app.k-dense.ai)** is
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**Get $50 in free credits** — no credit card required.
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<a href="https://app.k-dense.ai"><img src="https://img.shields.io/badge/Try_K--Dense_Web-Start_Free-blue?style=for-the-badge&logo=data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHdpZHRoPSIyNCIgaGVpZ2h0PSIyNCIgdmlld0JveD0iMCAwIDI0IDI0IiBmaWxsPSJub25lIiBzdHJva2U9IndoaXRlIiBzdHJva2Utd2lkdGg9IjIiIHN0cm9rZS1saW5lY2FwPSJyb3VuZCIgc3Ryb2tlLWxpbmVqb2luPSJyb3VuZCI+PHBhdGggZD0iTTUgMTJoMTQiLz48cGF0aCBkPSJtMTIgNSA3IDctNyA3Ii8+PC9zdmc+" alt="Try K-Dense Web"></a>
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<a href="https://k-dense.ai"><img src="https://img.shields.io/badge/Try_K--Dense_Web-Start_Free-blue?style=for-the-badge&logo=data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHdpZHRoPSIyNCIgaGVpZ2h0PSIyNCIgdmlld0JveD0iMCAwIDI0IDI0IiBmaWxsPSJub25lIiBzdHJva2U9IndoaXRlIiBzdHJva2Utd2lkdGg9IjIiIHN0cm9rZS1saW5lY2FwPSJyb3VuZCIgc3Ryb2tlLWxpbmVqb2luPSJyb3VuZCI+PHBhdGggZD0iTTUgMTJoMTQiLz48cGF0aCBkPSJtMTIgNSA3IDctNyA3Ii8+PC9zdmc+" alt="Try K-Dense Web"></a>
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*Learn more at [k-dense.ai](https://k-dense.ai)*
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*Learn more at [k-dense.ai](https://k-dense.ai)* | *[Read our detailed comparison →](https://k-dense.ai/blog/k-dense-web-vs-claude-scientific-skills)*
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---
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## 📦 What's Included
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This repository provides **139 scientific skills** organized into the following categories:
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This repository provides **140 scientific skills** organized into the following categories:
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- **28+ Scientific Databases** - Direct API access to OpenAlex, PubMed, bioRxiv, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, and more
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- **55+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, BioServices, PennyLane, Qiskit, and others
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@@ -88,7 +88,7 @@ Each skill includes:
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- [Getting Started](#getting-started)
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- [Claude Code](#claude-code-recommended)
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- [Cursor IDE](#cursor-ide)
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- [Any MCP Client](#any-mcp-client)
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- [Any MCP Client](#any-mcp-client-not-for-claude-code)
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- [Support Open Source](#heart-support-the-open-source-community)
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- [Prerequisites](#prerequisites)
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- [Quick Examples](#quick-examples)
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- **Multi-Step Workflows** - Execute complex pipelines with a single prompt
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### 🎯 **Comprehensive Coverage**
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- **139 Skills** - Extensive coverage across all major scientific domains
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- **140 Skills** - Extensive coverage across all major scientific domains
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- **28+ Databases** - Direct access to OpenAlex, PubMed, bioRxiv, ChEMBL, UniProt, COSMIC, and more
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- **55+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioServices, PennyLane, Qiskit, and others
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**Step 2: Register the Marketplace**
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In Claude Code, run the following command:
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```bash
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/plugin marketplace add K-Dense-AI/claude-scientific-skills
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```
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**Step 3: Install Skills**
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**Step 3: Install the Plugin**
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1. Open Claude Code
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**Option A: Direct Install (Fastest)**
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```bash
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/plugin install scientific-skills@claude-scientific-skills
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```
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**Option B: Interactive Install**
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1. Run `/plugin` in Claude Code
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2. Select **Browse and install plugins**
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3. Choose **claude-scientific-skills**
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3. Choose **claude-scientific-skills** marketplace
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4. Select **scientific-skills**
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5. Click **Install now**
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**That's it!** Claude will automatically use the appropriate skills when you describe your scientific tasks. Make sure to keep the skill up to date!
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**That's it!** Claude will automatically use the appropriate skills when you describe your scientific tasks.
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**Managing Your Plugin:**
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```bash
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# Check installed plugins
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/plugin → Manage Plugins
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# Update the plugin to the latest version
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/plugin update scientific-skills@claude-scientific-skills
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# Enable/disable the plugin
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/plugin enable scientific-skills@claude-scientific-skills
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/plugin disable scientific-skills@claude-scientific-skills
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# Uninstall if needed
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/plugin uninstall scientific-skills@claude-scientific-skills
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```
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---
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## 📚 Available Skills
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This repository contains **139 scientific skills** organized across multiple domains. Each skill provides comprehensive documentation, code examples, and best practices for working with scientific libraries, databases, and tools.
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This repository contains **140 scientific skills** organized across multiple domains. Each skill provides comprehensive documentation, code examples, and best practices for working with scientific libraries, databases, and tools.
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### Skill Categories
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- Genomic tools: gget, geniml, gtars, deepTools, FlowIO, Zarr
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- Phylogenetics: ETE Toolkit
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#### 🧪 **Cheminformatics & Drug Discovery** (10+ skills)
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#### 🧪 **Cheminformatics & Drug Discovery** (11+ skills)
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- Molecular manipulation: RDKit, Datamol, Molfeat
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- Deep learning: DeepChem, TorchDrug
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- Docking & screening: DiffDock
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- Cloud quantum chemistry: Rowan (pKa, docking, cofolding)
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- Drug-likeness: MedChem
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- Benchmarks: PyTDC
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### Contribution Guidelines
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✅ **Adhere to the [Agent Skills Specification](https://agentskills.io/specification)** — Every skill must follow the official spec (valid `SKILL.md` frontmatter, naming conventions, directory structure)
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✅ Maintain consistency with existing skill documentation format
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✅ Include practical, working examples in all contributions
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✅ Ensure all code examples are tested and functional
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✅ Follow scientific best practices in examples and workflows
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✅ Update relevant documentation when adding new capabilities
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**Problem: Skills not loading in Claude Code**
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- Solution: Ensure you've installed the latest version of Claude Code
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- Try reinstalling the plugin: `/plugin marketplace add K-Dense-AI/claude-scientific-skills`
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- Verify the plugin is installed: `/plugin → Manage Plugins`
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- Try reinstalling: `/plugin uninstall scientific-skills@claude-scientific-skills` then `/plugin install scientific-skills@claude-scientific-skills`
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- Re-add the marketplace if needed: `/plugin marketplace add K-Dense-AI/claude-scientific-skills`
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**Problem: Missing Python dependencies**
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- Solution: Check the specific `SKILL.md` file for required packages
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