671 projects whose own agent configuration covers scientific. These are not mods to install — they are how the maintainers of these repositories tell an agent what to do, and what to avoid.
All projects Building agents7,374Claude Code6,573Data and AI3,706Backend and APIs3,486Languages3,398Planning3,181Git and workflow3,100Code review2,701Memory and context2,354Testing2,311Research2,292DevOps and cloud2,282
Any agent Claude CodeCodexOpenCodeGitHub CopilotGemini CLICursorWindsurfKiro
| Project | Stars | Configures | Files | Always loaded |
|---|---|---|---|---|
| bigdataviewer/bigdataviewer-playground | 21 | Claude Code | 1 | 1,184 tok |
| CliMA/SurfaceFluxes.jl clima.github.io GPU-capable surface fluxes between atmosphere, ocean, and land via Monin-Obukhov Similarit | 21 | Codex, OpenCode | 1 | 1,330 tok |
| Beneficial-AI-Foundation/FloatSpec Formally Verified Float Implementation with lean4 | 21 | Claude Code, Codex, OpenCode | 2 | 7,741 tok |
| MattArtzAnthro/gephi-ai mattartz.me Extends Gephi with AI capabilities. Includes a Gephi plugin for graph analytics, an MCP se | 21 | Claude Code, Codex, Gemini CLI, OpenCode | 3 | 2,678 tok |
| yang3kc/daily_arxiv_digest Daily digest of interesting arXiv papers — an unattended LLM pipeline for cron, plus a zer | 21 | Claude Code, Codex, OpenCode | 2 | 1,792 tok |
| BeibaiDraco/maieusis Maieusis — inspectable scientific question development before analysis | 20 | Claude Code | 1 | — |
| emircbngl/blender-optics-simulator Blender add-on to design, simulate, align & render optical setups — live beam tracing, kin | 20 | Claude Code, Codex, OpenCode | 7 | 951 tok |
| gtr36/personal-health-graph A portable, structured health context system that makes every AI smarter about you. | 19 | Claude Code | 34 | 1,753 tok |
| nickzren/opentargets-mcp MCP server for Open Targets data | 19 | Claude Code, Codex, OpenCode | 2 | 680 tok |
| navisbio/AACT_clinicaltrials_MCP | 19 | Claude Code | 1 | 530 tok |
| machinavitalis/jaxonomy py.jaxonomy.com JAX-native simulation engine for hybrid dynamical systems — block-diagram modeling, ODE/DA | 19 | Claude Code, Codex, GitHub Copilot, Gemini CLI, OpenCode | 5 | 2,254 tok |
| SkyShannonProver/shannon-prover skyshannonprover.github.io LLM agents that write machine-checked cryptographic proofs in EasyCrypt (arXiv:2607.02847) | 19 | Claude Code, Codex, OpenCode | 4 | 2,653 tok |
| Hereon-InstituteMS/OASiS OASiS — an open-source agentic framework for verified multi-physics, multi-code simulation | 18 | GitHub Copilot, Cursor | 2 | 1,572 tok |
| natnew/awesome-ai-scientists natnew.github.io A curated collection of resources for building “AI Scientist” systems: AI that assists sci | 18 | Claude Code, Codex, OpenCode | 2 | 4,113 tok |
| huifer/drug-discovery-skills wellally.tech Drug Discovery Intelligence plugin for Claude Code. AI-powered target validation, competi | 18 | Claude Code | 1 | 814 tok |
| omar-A-hassan/medsci-agent Biomedical research agent with 28 MCP tools powered by MedGemma, TxGemma and OpenCode | 18 | Claude Code, GitHub Copilot, OpenCode | 31 | 907 tok |
| robertdcurrier/erddap2mcp ERDDAP interface to LLMs using MCP | 18 | Claude Code | 1 | 2,300 tok |
| edwnh/dqmc | 18 | Claude Code, Codex, OpenCode | 7 | 1,920 tok |
| AlessandroCaforio/Academic-Writing Multi-agent Claude Code workflow for writing an empirical economics Master thesis — 17 age | 17 | Claude Code | 12 | 5,883 tok |
| kimimgo/viznoir kimimgo.github.io VTK is all you need. AI-Ready VTK visualization for science and engineering. | 17 | Claude Code | 1 | 2,647 tok |
| goodfire-ai/evee-mcp MCP server for the EVEE (Evo Variant Effect Explorer) API — variant effect prediction from | 17 | Claude Code | 1 | — |
| cybertronai/SutroYaro cybertronai.github.io SutroYaro — Sutro Group research workspace for energy-efficient AI training. Point any cod | 16 | Claude Code, Codex, Gemini CLI, OpenCode | 14 | 7,023 tok |
| olavocarvalho/vscode-runtime-notebook-mcp Embedded MCP server for the VS Code Jupyter runtime: edit cells, run code, fetch outputs. | 16 | Claude Code | 1 | 879 tok |
| bigbio/sdrf-skills sdrf.quantms.org Agentic plugins to annotate SDRF using Claude; Codex; Cursor; Gemini | 16 | Claude Code, Gemini CLI | 2 | 6,449 tok |
| HolobiomicsLab/asb-skill-collections holobiomicslab.cnrs.fr Curated, evidence-grounded skill and software-tool collections for scientific AI agents, g | 15 | Claude Code, Codex, GitHub Copilot, OpenCode | 3 | 2,554 tok |
| nickzren/biomed-agent Connecting AI to biomedical data | 15 | Claude Code, Codex, OpenCode | 2 | 1,135 tok |
| Agnuxo1/p2pclaw-mcp-server p2pclaw.com MCP server + REST API for the P2PCLAW decentralized AI research network. Lets agents publi | 15 | Claude Code | 1 | 2,252 tok |
| chemrich/MCPymol mcp server for pymol for conversational protein display | 15 | Claude Code | 1 | — |
| XBP-Europe/sagemath-mcp pypi.org Stateful SageMath MCP server: 37 tools for symbolic math, algebra, number theory, graphs a | 14 | Claude Code, Codex, OpenCode | 2 | 3,764 tok |
| andikarachman/data-science-plugin Data science and ML workflow tools for Claude Code. 6 agents, 4 commands, 6 skills for pro | 14 | Claude Code | 1 | 1,378 tok |
| SHSharkar/MCP-Mathematics pypi.org A comprehensive Model Context Protocol (MCP) server that turns any AI assistant into a pow | 14 | Claude Code | 1 | 3,117 tok |
| calebzu/pmsm-control-claude-skills-for-matlab PMSM Claude Skills: methodology + skill library for AI-augmented MATLAB/Simulink modeling | 13 | Claude Code | 1 | 1,096 tok |
| BnJam/stac-mcp An MCP Server for STAC requests | 13 | Codex, GitHub Copilot, OpenCode | 2 | 5,711 tok |
| yusong652/yade-mcp pypi.org MCP server connecting AI agents to YADE — run DEM simulations through natural conversation | 13 | Claude Code, Codex, OpenCode | 2 | 1,379 tok |
| James-Traina/compound-science Research workflow toolkit for structural econometrics, causal inference, game theory, and | 13 | Claude Code | 1 | 2,386 tok |
| dbcls/togomcp togomcp.rdfportal.org MCP server for life-science knowledge graphs | 13 | Claude Code | 9 | 3,924 tok |
| maweiruc/stat-toolkits-eif Documentation-first toolkit for deriving, validating, and auditing efficient influence fun | 13 | Codex, OpenCode | 1 | 1,072 tok |
| reason-healthcare/rh-skills An agentic workflow toolset providing superpowers for healthcare informaticists | 12 | Claude Code, Codex, OpenCode | 22 | 1,128 tok |
| Xinyang-Li666/SciCrucible A Claude-based scientific intelligence knowledge base covering the full cycle from literat | 12 | Claude Code | 10 | 1,107 tok |
| u9401066/med-paper-assistant u9401066.github.io Auditable MCP + cross-agent harness for autonomous and human-guided academic writing—from | 12 | Claude Code, Codex, GitHub Copilot, OpenCode | 50 | 8,475 tok |
| jurimaxam-dotcom/chemdraw-mcp MCP server for Claude: molecule names or SMILES → publication-style 2D structure drawings | 12 | Claude Code | 1 | 3,342 tok |
| koljaschoepe/scientific-writing KI-gestütztes Framework für wissenschaftliche Arbeiten mit Claude Code. Seminararbeiten bi | 11 | Claude Code | 26 | 1,163 tok |
| jimezsa/opencolab opencolab.ai 🐙 Accelerating Scientific Discovery — Turn your research into an always-on autonomous lab | 11 | Claude Code, Codex, Gemini CLI, OpenCode | 3 | 5,041 tok |
| MustafaKadhim/Coding-Agent-Guidelines-Radiotherapy This is my personal coding guidelines optimized for radiotherapy research and inspired by | 11 | Claude Code, Codex, OpenCode | 2 | 4,472 tok |
| markusl/statfin-mcp markusl.github.io Production-grade Model Context Protocol (MCP) server for Statistics Finland's StatFin data | 11 | Claude Code | 1 | 802 tok |
| OATH-md/OathMCP mcp.oath.md Agent-native MCP server for evidence-backed clinical calculators. | 11 | Codex, OpenCode | 2 | 1,920 tok |
| Rezenders/scientific_writing_agent Template repo with agent's configuration for working in scientific papers | 11 | Claude Code, Codex, OpenCode | 2 | 3,489 tok |
| ai-analyst-lab/agentxp Open-source system for the design and analysis of controlled experiments, intended for use | 11 | Claude Code | 6 | 3,971 tok |
| kucherenko/petropowers AI skills framework for petroleum engineering workflows, built on Superpowers foundation. | 11 | Claude Code, Codex, Gemini CLI, OpenCode | 3 | 1,347 tok |
| dengxu11111/dual-ai-paper-coach Claude Code writes the paper. Codex CLI independently reviews it. Together they produce a | 11 | Claude Code, Codex, OpenCode | 10 | 3,597 tok |