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Added ISO 13485 certification prep skill
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Timothy Kassis
71
README.md
71
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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> 💼 For substantially more advanced capabilities, compute infrastructure, and enterprise-ready offerings, check out [k-dense.ai](https://k-dense.ai/).
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A comprehensive collection of **125+ ready-to-use scientific skills** for Claude, created by the K-Dense team. 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 **138 ready-to-use scientific skills** for Claude, created by the K-Dense team. 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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These skills enable Claude to seamlessly work with specialized scientific libraries, databases, and tools across multiple scientific domains:
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- 🧬 Bioinformatics & Genomics - Sequence analysis, single-cell RNA-seq, gene regulatory networks, variant annotation, phylogenetic analysis
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- 🧪 Cheminformatics & Drug Discovery - Molecular property prediction, virtual screening, ADMET analysis, molecular docking, lead optimization
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- 🔬 Proteomics & Mass Spectrometry - LC-MS/MS processing, peptide identification, spectral matching, protein quantification
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- 🏥 Clinical Research & Precision Medicine - Clinical trials, pharmacogenomics, variant interpretation, drug safety, precision therapeutics
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- 🏥 Clinical Research & Precision Medicine - Clinical trials, pharmacogenomics, variant interpretation, drug safety, clinical decision support, treatment planning
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- 🧠 Healthcare AI & Clinical ML - EHR analysis, physiological signal processing, medical imaging, clinical prediction models
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- 🖼️ Medical Imaging & Digital Pathology - DICOM processing, whole slide image analysis, computational pathology, radiology workflows
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- 🤖 Machine Learning & AI - Deep learning, reinforcement learning, time series analysis, model interpretability, Bayesian methods
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- 🔮 Materials Science & Chemistry - Crystal structure analysis, phase diagrams, metabolic modeling, computational chemistry
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- 🌌 Physics & Astronomy - Astronomical data analysis, coordinate transformations, cosmological calculations, symbolic mathematics, physics computations
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- ⚙️ Engineering & Simulation - Discrete-event simulation, multi-objective optimization, metabolic engineering, systems modeling, process optimization
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- 📊 Data Analysis & Visualization - Statistical analysis, network analysis, time series, publication-quality figures, large-scale data processing
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- 📊 Data Analysis & Visualization - Statistical analysis, network analysis, time series, publication-quality figures, large-scale data processing, EDA
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- 🧪 Laboratory Automation - Liquid handling protocols, lab equipment control, workflow automation, LIMS integration
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- 📚 Scientific Communication - Literature review, peer review, scientific writing, document processing, publication workflows
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- 📚 Scientific Communication - Literature review, peer review, scientific writing, document processing, posters, slides, schematics, citation management
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- 🔬 Multi-omics & Systems Biology - Multi-modal data integration, pathway analysis, network biology, systems-level insights
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- 🧬 Protein Engineering & Design - Protein language models, structure prediction, sequence design, function annotation
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- 🎓 Research Methodology - Hypothesis generation, scientific brainstorming, critical thinking, grant writing, scholar evaluation
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**Transform Claude Code into an 'AI Scientist' on your desktop!**
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@@ -32,12 +33,13 @@ These skills enable Claude to seamlessly work with specialized scientific librar
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## 📦 What's Included
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This repository provides **125+ scientific skills** organized into the following categories:
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This repository provides **138 scientific skills** organized into the following categories:
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- **26+ Scientific Databases** - Direct API access to OpenAlex, PubMed, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, and more
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- **54+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, PennyLane, Qiskit, and others
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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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- **15+ Scientific Integrations** - Benchling, DNAnexus, LatchBio, OMERO, Protocols.io, and more
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- **20+ Analysis & Communication Tools** - Literature review, scientific writing, peer review, document processing
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- **30+ Analysis & Communication Tools** - Literature review, scientific writing, peer review, document processing, posters, slides, schematics, and more
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- **10+ Research & Clinical Tools** - Hypothesis generation, grant writing, clinical decision support, treatment plans, regulatory compliance
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Each skill includes:
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- ✅ Comprehensive documentation (`SKILL.md`)
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- **Multi-Step Workflows** - Execute complex pipelines with a single prompt
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### 🎯 **Comprehensive Coverage**
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- **125+ Skills** - Extensive coverage across all major scientific domains
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- **26+ Databases** - Direct access to OpenAlex, PubMed, ChEMBL, UniProt, COSMIC, and more
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- **54+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, PennyLane, Qiskit, and others
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- **138 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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### 🔧 **Easy Integration**
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- **One-Click Setup** - Install via Claude Code or MCP server
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## 📚 Available Skills
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This repository contains **125+ 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 **138 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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#### 🧬 **Bioinformatics & Genomics** (15+ skills)
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- Sequence analysis: BioPython, pysam, scikit-bio
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#### 🧬 **Bioinformatics & Genomics** (16+ skills)
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- Sequence analysis: BioPython, pysam, scikit-bio, BioServices
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- Single-cell analysis: Scanpy, AnnData, scvi-tools, Arboreto, Cellxgene Census
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- Genomic tools: gget, geniml, gtars, deepTools, FlowIO, Zarr
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- Phylogenetics: ETE Toolkit
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#### 🔬 **Proteomics & Mass Spectrometry** (2 skills)
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- Spectral processing: matchms, pyOpenMS
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#### 🏥 **Clinical Research & Precision Medicine** (8+ skills)
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#### 🏥 **Clinical Research & Precision Medicine** (12+ skills)
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- Clinical databases: ClinicalTrials.gov, ClinVar, ClinPGx, COSMIC, FDA Databases
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- Healthcare AI: PyHealth, NeuroKit2
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- Healthcare AI: PyHealth, NeuroKit2, Clinical Decision Support
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- Clinical documentation: Clinical Reports, Treatment Plans
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- Variant analysis: Ensembl, NCBI Gene
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#### 🖼️ **Medical Imaging & Digital Pathology** (3 skills)
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- Discrete-event simulation: SimPy
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- Data processing: Dask, Polars, Vaex
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#### 📊 **Data Analysis & Visualization** (10+ skills)
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- Visualization: Matplotlib, Seaborn, Plotly
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#### 📊 **Data Analysis & Visualization** (14+ skills)
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- Visualization: Matplotlib, Seaborn, Plotly, Scientific Visualization
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- Geospatial analysis: GeoPandas
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- Network analysis: NetworkX
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- Symbolic math: SymPy
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- PDF generation: ReportLab
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- Data access: Data Commons
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- Exploratory data analysis: EDA workflows
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- Statistical analysis: Statistical Analysis workflows
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#### 🧪 **Laboratory Automation** (3 skills)
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- Liquid handling: PyLabRobot
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- Protein language models: ESM
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- Cloud laboratory platform: Adaptyv (automated protein testing and validation)
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#### 📚 **Scientific Communication** (10+ skills)
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- Literature: OpenAlex, PubMed, Literature Review
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#### 📚 **Scientific Communication** (20+ skills)
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- Literature: OpenAlex, PubMed, bioRxiv, Literature Review
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- Web search: Perplexity Search (AI-powered search with real-time information)
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- Writing: Scientific Writing, Peer Review
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- Document processing: XLSX, MarkItDown
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- Publishing: Paper-2-Web
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- Document processing: XLSX, MarkItDown, Document Skills
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- Publishing: Paper-2-Web, Venue Templates
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- Presentations: Scientific Slides, LaTeX Posters, PPTX Posters
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- Diagrams: Scientific Schematics
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- Citations: Citation Management
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- Illustration: Generate Image (AI image generation with FLUX.2 Pro and Gemini 3 Pro (Nano Banana Pro))
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#### 🔬 **Scientific Databases** (27+ skills)
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#### 🔬 **Scientific Databases** (28+ skills)
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- Protein: UniProt, PDB, AlphaFold DB
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- Chemical: PubChem, ChEMBL, DrugBank, ZINC, HMDB
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- Genomic: Ensembl, NCBI Gene, GEO, ENA, GWAS Catalog
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- Literature: bioRxiv (preprints)
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- Clinical: ClinVar, COSMIC, ClinicalTrials.gov, ClinPGx, FDA Databases
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- Pathways: KEGG, Reactome, STRING
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- Targets: Open Targets
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- Enzymes: BRENDA
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- Patents: USPTO
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#### 🔧 **Infrastructure & Platforms** (5+ skills)
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#### 🔧 **Infrastructure & Platforms** (6+ skills)
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- Cloud compute: Modal
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- Genomics platforms: DNAnexus, LatchBio
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- Microscopy: OMERO
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- Automation: Opentrons
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- Tool discovery: ToolUniverse
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- Tool discovery: ToolUniverse, Get Available Resources
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#### 🎓 **Research Methodology & Planning** (8+ skills)
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- Ideation: Scientific Brainstorming, Hypothesis Generation
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- Critical analysis: Scientific Critical Thinking, Scholar Evaluation
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- Funding: Research Grants
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- Discovery: Research Lookup
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- Market analysis: Market Research Reports
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#### ⚖️ **Regulatory & Standards** (1 skill)
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- Medical device standards: ISO 13485 Certification
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> 📖 **For complete details on all skills**, see [docs/scientific-skills.md](docs/scientific-skills.md)
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