科学智能代理

Scientific Agent Skills

🔔 Claude Scientific Skills is now Scientific Agent Skills. Same skills, broader compatibility — now works with any AI agent that supports the open Agent Skills standard, not just Claude.

New: K-Dense BYOK — A free, open-source AI co-scientist that runs on your desktop, powered by Scientific Agent Skills. Bring your own API keys, pick from 40+ models, and get a full research workspace with web search, file handling, 100+ scientific databases, and access to all 177 skills in this repo. Your data stays on your computer, and you can optionally scale to cloud compute via Modal for heavy workloads. Get started here.

🎥 Webinar recording — Getting Started with K-Dense BYOK A hands-on walkthrough of K-Dense BYOK, our free, open-source AI co-scientist that runs locally on your own machine and is powered by Scientific Agent Skills. We cover how to set it up, bring your own API keys, and run real research workflows with these skills. No prior technical experience needed. Watch the recording →

Stay up to date: Follow K-Dense on X, LinkedIn, YouTube, and Reddit for new skills, release announcements, walkthroughs, research workflow demos, and examples you can use with your own AI agent.

📄 Paper: Scientific Agent Skills is described in Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents (arXiv:2609.00065). If you use these skills in your research, please cite the paper.

A collection of 177 scientific and research skills for AI agents, created by K-Dense. The skills cover biology, chemistry, medicine, physics, engineering, Earth science, data analysis, and scientific communication. Each provides guidance for a specific package, data source, or workflow, including the scientific conventions and validation checks needed to use it.

The collection follows the open Agent Skills standard and works with Cursor, Claude Code, Codex, Google Antigravity, and other compatible hosts. It is also a portable Agent Plugins package (plugin.json + skills/), so clients that support that standard can load the collection as one plugin. Browse the illustrated skill guides, skill categories, or complete catalog to choose the skills relevant to your work.

⭐ Help make AI for science easier to discover: If Scientific Agent Skills saves you time, teaches your agent a workflow, or helps your lab move faster, please star this repository. A star is a public signal that these open, reusable research skills are worth maintaining: it helps scientists, engineers, and open-source contributors find the project, shows which agent-skill standards are gaining real adoption, and gives us a clear reason to keep expanding the collection for the community.

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These skills enable your AI agent to seamlessly work with specialized scientific libraries, databases, and tools across multiple scientific domains. While the agent can use any Python package or API on its own, these explicitly defined skills provide curated documentation and examples that make it significantly stronger and more reliable for the workflows below: - 🧬 Bioinformatics & Genomics - Sequence analysis, single-cell RNA-seq, pooled CRISPR screens, primer design, amplicon microbiomes, variant annotation, phylogenetics - 🧪 Cheminformatics & Drug Discovery - Molecular property prediction, virtual screening, ADMET analysis, molecular docking, lead optimization, calibrated 1D NMR processing - 🔬 Proteomics & Mass Spectrometry - LC-MS/MS processing, peptide identification, spectral matching, protein quantification - 🏥 Clinical Research & Evidence Workflows - Clinical trials, pharmacogenomics, variant evidence review, pharmacokinetic/pharmacodynamic modelling and dose-regimen evaluation, aggregate decision-support evaluation, source-bound draft report structures, and formatting of clinician-authored treatment decisions - 🧠 Healthcare AI & Biosignal Research - EHR and model research, physiological signal analysis, and retrospective validation—not patient-specific diagnosis, treatment, alarms, or deployment decisions - 🐭 Preclinical Research & Animal Welfare - Multivariate severity scoring and humane-endpoint forecasting for laboratory animal studies, for 3Rs/refinement analysis and EU Directive 2010/63/EU reporting—an aid to severity assessment, never a decision rule - 🖼️ Microscopy, Medical Imaging & Digital Pathology - Quantitative fluorescence microscopy, privacy-aware DICOM processing, research-only whole-slide image analysis, computational pathology, and radiology data workflows - 🧠 Neuroscience & Electrophysiology - BIDS datasets, NWB conversion and clock alignment, extracellular recordings, and physiological signals - 🤖 Machine Learning & AI - Deep learning, reinforcement learning, time series analysis, model interpretability, Bayesian methods - 🔮 Materials Science & Chemistry - Crystal structure analysis, CALPHAD phase equilibria, metabolic modeling, computational chemistry - 🌌 Physics & Astronomy - Astronomical data analysis, coordinate transformations, cosmological calculations, symbolic mathematics, physics computations - ⚙️ Engineering & Simulation - Battery cycling models, chemical kinetics and ignition delay, fluid dynamics, lab hardware CAD and custom-part fabrication, discrete-event simulation, process optimization - 📊 Data Analysis & Visualization - Statistical analysis, network analysis, time series, publication-quality figures, large-scale data processing, EDA - 🌊 Chemical Oceanography - Seawater carbonate chemistry, ocean acidification, mineral saturation, and measurement uncertainty - 🌍 Geospatial Science & Remote Sensing - Satellite imagery processing, GIS analysis, spatial statistics, terrain analysis, machine learning for Earth observation - 🧪 Laboratory Automation - Liquid handling protocols, lab equipment control, workflow automation, LIMS integration - 📚 Scientific Communication - Evidence-traceable writing, confidential authorized peer review, literature synthesis, document processing, macro-free PPTX posters, slides, schematics, and citation management - 🔬 Multi-omics & Systems Biology - Multi-modal data integration, pathway analysis, carbon-13 metabolic flux inference, biochemical kinetic models - 🧬 Protein Engineering & Design - Protein language models, structure prediction, cryo-EM refinement, sequence design, function annotation - 🧰 Agent Platforms & Infrastructure - Build on Pi with SDK, RPC, extensions, custom providers/models, packages, TUI components, and session tooling - 🎓 Research Methodology - Evidence-bounded candidate hypotheses, scientific brainstorming, critical thinking, grant writing, and qualitative low-stakes evaluation of scholarly works - ⚖️ Regulatory & Standards - Draft evidence-preparation artifacts for ISO management-system and laboratory standards, plus analytical method validation, verification, and transfer under ICH/USP/CLSI frameworks—prepared for qualified review, never a certification, accreditation, or method-release decision

Transform your AI coding agent into an 'AI Scientist' on your desktop!

🎬 New to Scientific Agent Skills? Watch our Getting Started with Scientific Agent Skills video for a quick walkthrough.

📦 What's Included

This repository provides 177 scientific and research skills organized into the following categories:

• 100+ Scientific & Financial Databases - The Database Lookup skill documents 80 databases with public, registered, or licensed access (PubChem, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, FRED, USPTO, and more), including endpoint selection, pagination, and provenance. Dedicated skills cover DepMap, Imaging Data Commons, PrimeKG, NCATS ARAX, U.S. Treasury Fiscal Data, Hugging Science, OneKGPd, Genomic Intelligence, and AlphaGenome. Multi-database packages such as BioServices, Biopython, and gget add further coverage
• 70+ Optimized Python Package Skills - Explicitly defined, version-aware workflows for RDKit, Scanpy, PyTorch Lightning, scikit-learn, PyTDC, PathML, pydicom, NeuroKit2, PufferLib, QuTiP, GeoPandas, pymatgen, BioPython, Qiskit, Molecular Dynamics (OpenMM/MDAnalysis), and others. The agent can still use any Python package; these skills provide stronger, safer guidance for the packages listed
• 9 Scientific Integration Skills - Explicitly defined skills for Benchling, DNAnexus, LatchBio, OMERO, Protocols.io, Open Notebook, Ginkgo Cloud Lab, LabArchives, and Opentrons. Again, the agent is not limited to these — any API or platform reachable from Python is fair game; these skills are the optimized, pre-documented paths
• 30+ Analysis & Communication Tools - Literature review, evidence-traceable scientific writing, confidential peer review, document processing, Paperclip (full-text papers, FDA/PMDA/EMA filings, and trial registries with line-pinned citations), Paperzilla, Exa Search, macro-free PPTX posters, slides, schematics, infographics, Mermaid diagrams, and more
• 10+ Research & Clinical Tools - Evidence-bounded hypothesis generation, grant writing, aggregate clinical decision-support research, clinician-authored treatment-plan formatting, PK/PD modelling and simulation (NCA, population PK, exposure-response, bioequivalence, first-in-human dose), BIDS, ISO standards-readiness evidence preparation (ISO 13485, ISO 14971, ISO/IEC 17025, ISO 15189), analytical method validation and transfer (ICH Q2(R2)/Q14, ICH M10, USP, CLSI EP), scenario analysis, and workflow-derived skill drafting with Autoskill

Every skill has a SKILL.md with its purpose, workflow, and version metadata. Depending on the workflow, it also includes code examples, reference documentation, executable helpers, or templates. Skills with bundled scripts/ have a corresponding test suite under tests/<skill-name>/ and a dependency entry in tests/skill-requirements.toml.

What's new in 2.72.0

The docx, pdf, pptx, and xlsx document skills, which were vendored from anthropics/skills under Anthropic's own license, are no longer bundled. The collection now has 177 skills; install those four from Anthropic's repository if you rely on them. Scientific Slides now builds PowerPoint decks with PptxGenJS or python-pptx and reviews them through LibreOffice and its own rendering and validation scripts.

What's new in 2.71.0

This update refreshes all 181 skills, including package and API guidance, dependency requirements, reference documentation, and validation workflows. Highlights include:

• Database retrieval: Database Lookup now catalogs 80 sources, with access requirements, retrieval contracts, and provenance checks.
• Package compatibility: Updated documented baselines include PathML 3.0.8, GeoPandas 1.2.0, and build123d 0.13.0 for lab hardware CAD. PufferLib distinguishes native 5.0, PyPI 3.0.0, and historical 4.0 workflows.
• Image generation and agent tooling: Generate Image uses the OpenRouter Image API with model discovery and request validation. Pi Agent documents Pi 0.99.2, native MCP, and updated ecosystem packages.
• RNA-seq workflow boundaries: Bulk RNA-seq prepares reads and validated counts for a PyDESeq2 handoff; Pathway Enrichment covers downstream enrichment.

Each skill records its own compatibility requirements and validation scope. Check those details before reusing an older workflow; local tests, live-service checks, and illustrative examples have different coverage.