---
title: "scientific-agent-skills"
description: "Ready-to-use scientific and research Agent Skills for biology, chemistry, medicine, and related workflows."
canonical: https://agentpluginsdirectory.com/plugins/scientific-agent-skills
last-updated: 2026-09-26
---

# scientific-agent-skills
Ready-to-use scientific and research Agent Skills for biology, chemistry, medicine, and related workflows.
- Slug: scientific-agent-skills
- Publisher: K-Dense Inc.
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Manifest: plugin.json
- Version: 2.69.0
- License: MIT
- Category (editorial): research
- Skills: 166 (adaptyv, aeon, alphagenome, analytical-method-validation, anndata, arbor, arboreto, astropy, autoskill, benchling-integration, bgpt-paper-search, bids, biopython, bioservices, bulk-rnaseq, cellxgene-census, cirq, citation-management, clinical-decision-support, clinical-reports, cobrapy, consciousness-council, dask, database-lookup, datalad, datamol, deepchem, deepspot-m, deeptools, depmap, dhdna-profiler, diffdock, dnanexus-integration, docx, esm, etetoolkit, exa-search, experimental-design, exploratory-data-analysis, flowio, fluidsim, folklore-variant-evidence, generate-image, geniml, genomic-coordinates, genomic-intelligence, geomaster, geopandas, get-available-resources, gget, ginkgo-cloud-lab, glycoengineering, gtars, histolab, hugging-science, hypogenic, hypothesis-generation, imaging-data-commons, infographics, iso-standards-readiness, lab-hardware-cad, labarchive-integration, lamindb, latchbio-integration, latex-posters, liteparse, literature-review, markdown-mermaid-writing, market-research-reports, markitdown, matchms, matlab, matplotlib, medchem, modal, molecular-dynamics, molfeat, ncats-arax, networkx, neurokit2, neuropixels-analysis, nextflow, omero-integration, onekgpd, ontology-term-resolution, open-notebook, openpiv, opentrons-integration, optimize-for-gpu, pacsomatic, paper-lookup, paperclip, paperzilla, parallel-web, pathml, pathogen-variant-surveillance, pathway-enrichment, pdf, peer-review, pennylane, phylogenetics, pi-agent, pkpd-modeling, polars-bio, polars, pptx-posters, pptx, primekg, protocolsio-integration, pufferlib, pydeseq2, pydicom, pyhealth, pylabrobot, pymatgen, pymc, pymoo, pyopenms, pysam, pytdc, pytorch-lightning, pyzotero, qiskit, qutip, rdkit, relsa-severity-assessment, research-grants, research-lookup, rowan, scanpy, scholar-evaluation, scientific-brainstorming, scientific-critical-thinking, scientific-schematics, scientific-slides, scientific-visualization, scientific-writing, scikit-bio, scikit-learn, scikit-survival, scvelo, scvi-tools, seaborn, shap, simpy, stable-baselines3, statistical-analysis, statistical-power, statsmodels, sympy, tamarind, tiledbvcf, timesfm-forecasting, torch-geometric, torchdrug, transformers, treatment-plans, umap-learn, uncertainty-and-units, usfiscaldata, vaex, venue-templates, waypoint-bio, what-if-oracle, xlsx, zarr-python)
- MCP servers: 0
- Stars: 46692
- Repository created: 2025-10-19
- Repository last pushed: 2026-09-21
- Publisher type: Organization
- Listing: https://agentpluginsdirectory.com/plugins/scientific-agent-skills
- Schema: https://agent-plugins.org/schemas/1.0.0/plugin.schema.json

## What scientific-agent-skills does, in the publisher's words

> 🔔 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 163 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.

From the project README, punctuation lightly normalized. Full text: https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/README.md

## Skills

- adaptyv: How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit p…
- aeon: This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algori…
- alphagenome
- analytical-method-validation: Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework, ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligan…
- anndata: Data structure for annotated matrices in single-cell analysis. Use when working with.h5ad files or integrating with the scverse ecosystem. This is the data format skill: for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
- arbor: Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without over…
- arboreto: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed com…
- astropy: Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.
- autoskill: Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose…
- benchling-integration: Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.
- bgpt-paper-search: Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experiment…
- bids: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing…
- biopython: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service inte…
- bioservices
- bulk-rnaseq
- cellxgene-census
- cirq
- citation-management
- clinical-decision-support
- clinical-reports
- cobrapy
- consciousness-council
- dask
- database-lookup
- datalad
- datamol
- deepchem
- deepspot-m
- deeptools
- depmap
- dhdna-profiler
- diffdock
- dnanexus-integration
- docx
- esm
- etetoolkit
- exa-search
- experimental-design
- exploratory-data-analysis
- flowio
- fluidsim
- folklore-variant-evidence
- generate-image
- geniml
- genomic-coordinates
- genomic-intelligence
- geomaster
- geopandas
- get-available-resources
- gget
- ginkgo-cloud-lab
- glycoengineering
- gtars
- histolab
- hugging-science
- hypogenic
- hypothesis-generation
- imaging-data-commons
- infographics
- iso-standards-readiness
- lab-hardware-cad
- labarchive-integration
- lamindb
- latchbio-integration
- latex-posters
- liteparse
- literature-review
- markdown-mermaid-writing
- market-research-reports
- markitdown
- matchms
- matlab
- matplotlib
- medchem
- modal
- molecular-dynamics
- molfeat
- ncats-arax
- networkx
- neurokit2
- neuropixels-analysis
- nextflow
- omero-integration
- onekgpd
- ontology-term-resolution
- open-notebook
- openpiv
- opentrons-integration
- optimize-for-gpu
- pacsomatic
- paper-lookup
- paperclip
- paperzilla
- parallel-web
- pathml
- pathogen-variant-surveillance
- pathway-enrichment
- pdf
- peer-review
- pennylane
- phylogenetics
- pi-agent
- pkpd-modeling
- polars-bio
- polars
- pptx-posters
- pptx
- primekg
- protocolsio-integration
- pufferlib
- pydeseq2
- pydicom
- pyhealth
- pylabrobot
- pymatgen
- pymc
- pymoo
- pyopenms
- pysam
- pytdc
- pytorch-lightning
- pyzotero
- qiskit
- qutip
- rdkit
- relsa-severity-assessment
- research-grants
- research-lookup
- rowan
- scanpy
- scholar-evaluation
- scientific-brainstorming
- scientific-critical-thinking
- scientific-schematics
- scientific-slides
- scientific-visualization
- scientific-writing
- scikit-bio
- scikit-learn
- scikit-survival
- scvelo
- scvi-tools
- seaborn
- shap
- simpy
- stable-baselines3
- statistical-analysis
- statistical-power
- statsmodels
- sympy
- tamarind
- tiledbvcf
- timesfm-forecasting
- torch-geometric
- torchdrug
- transformers
- treatment-plans
- umap-learn
- uncertainty-and-units
- usfiscaldata
- vaex
- venue-templates
- waypoint-bio
- what-if-oracle
- xlsx
- zarr-python

Descriptions come from the frontmatter of each SKILL.md, punctuation lightly normalized.