329 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 |
|---|---|---|---|---|
| Synthyra/FastPLMs Easy to use and efficient implementations of Protein Language Models | 51 | Claude Code, Codex, OpenCode | 2 | 2,041 tok |
| oqtopus-team/qdash oqtopus-team.github.io QDash: Large-scale QPU Calibration Platform | 51 | Claude Code, Codex, OpenCode | 3 | 2,453 tok |
| agjs/gb10-clock-cap Capping GPU clocks on NVIDIA GB10: -12C peak temp, -36% GPU power, ~1.6% throughput cost. | 50 | Codex, OpenCode | 1 | 1,319 tok |
| cqframework/clinical-reasoning cqframework.org CQF Clinical Reasoning on FHIR for Java | 49 | Claude Code, Codex, OpenCode | 3 | 930 tok |
| Dicklesworthstone/frankensim Plan-first Rust continuum for certified geometry, physics simulation, optimization, and re | 49 | Codex, OpenCode | 1 | 9,289 tok |
| xi-zhao/OpenQuantum Open-source quantum Agent workspace with a desktop client, Web UI, messaging, Qiskit/MCP t | 48 | Claude Code, Codex, OpenCode | 12 | 3,150 tok |
| AbhiRawat4841/mathematica-mcp Model Context Protocol (MCP) server that connects AI agents (Claude, Cursor, etc.) to Wolf | 48 | Codex, OpenCode | 1 | 533 tok |
| steel-dev/leaderboard leaderboard.steel.dev Open leaderboard for browser agents | 48 | Claude Code, Codex, OpenCode | 2 | 630 tok |
| life-itself/climate climate.lifeitself.org 🌍🔥 Life Itself's ongoing inquiry into the climate crisis | 48 | Claude Code, Codex, OpenCode | 4 | 1,196 tok |
| csml-rpi/AI-CFD-Scientist | 48 | Claude Code, Codex, OpenCode | 2 | 4,178 tok |
| jvogan/motif jvogan.github.io An AI-native molecular biology workbench for Claude Science: Claude opens sequence files a | 47 | Codex, OpenCode | 1 | 984 tok |
| Jyx0208/claude-science-api-bridge A local macOS proxy and installer that connects Claude Science to third-party APIs such as | 46 | Codex, OpenCode | 1 | 1,090 tok |
| soo-jeongkim/co-pymol PyMOL plugin - drive PyMOL from Claude Code, Cursor, or any MCP client. | 44 | Codex, OpenCode | 1 | 3,921 tok |
| letitbk/claude-academic-setup Claude Code + Cursor setup for academic social science researchers (R, Stata, Python). 22 | 43 | Claude Code, Codex, OpenCode | 2 | 805 tok |
| QinxiangCao/QualifiedCProgramming QCP (Qualified C Programming), a C program verification tool | 43 | Claude Code, Codex, OpenCode | 7 | 4,998 tok |
| alti3/stk-mcp An MCP server allowing LLMs to interact with Ansys/AGI STK - Digital Mission Engineering S | 42 | Codex, OpenCode | 1 | 288 tok |
| LaplaceYoung/ansys-aedt-mcp MCP server for Ansys Electronics Desktop automation with PyAEDT, HFSS, Maxwell, Q3D, Icepa | 42 | Codex, OpenCode | 1 | 182 tok |
| dhicoc/wuyun-liuqi-skills Five Movements and Six Qi Skills Router — AI auto-routing + deterministic calculation engi | 41 | Claude Code, Codex, OpenCode | 3 | 1,562 tok |
| piebro/openstreetmap-statistics piebro.github.io Monthly updated interactive statistics about OpenStreetMap. | 40 | Codex, OpenCode | 1 | 5,736 tok |
| voxel51/fiftyone-skills | 39 | Codex, OpenCode | 1 | 5,844 tok |
| yusong652/flac-mcp pypi.org MCP server connecting AI agents to ITASCA FLAC — run continuum simulations through natural | 39 | Claude Code, Codex, Gemini CLI, OpenCode | 3 | 3,549 tok |
| Patrick-Healy/tikz-diagrams-skill | 39 | Claude Code, Codex, GitHub Copilot, Gemini CLI, OpenCode | 5 | 589 tok |
| issol14/paper2code-skill A Claude Code Skill that converts research papers into executable code - no extra API cost | 38 | Codex, OpenCode | 1 | 998 tok |
| NatLabRockies/openstudio-mcp | 31 | Claude Code, Codex, OpenCode | 19 | 2,866 tok |
| ai-freer/fortune-skill Chinese traditional fortune-telling AI skill (BaZi 八字 + Zi Wei Dou Shu 紫微斗数) for Claude Co | 28 | Claude Code, Codex, OpenCode | 2 | 1,467 tok |
| ProfSynapse/Synaptic-Tuner | 27 | Claude Code, Codex, OpenCode | 14 | 6,355 tok |
| u9401066/pubmed-search-mcp u9401066.github.io MCP SDK v2 server for PubMed and multi-source biomedical research, with resilient search, | 27 | Claude Code, Codex, GitHub Copilot, OpenCode | 45 | 8,398 tok |
| nebius/nebius-physical-ai | 27 | Claude Code, Codex, Cursor, OpenCode | 3 | 5,768 tok |
| phisanti/MCPR phisanti.github.io MCPR enables AI agents to participate in interactive R sessions for professional analysis | 26 | Claude Code, Codex, OpenCode | 2 | 3,219 tok |
| sou350121/Spatial-Intelligence-Handbook kensou.mintlify.app A cross-embodiment handbook on spatial intelligence — compares SLAM / VIO / 3D representat | 26 | Codex, OpenCode | 1 | 6,856 tok |
| ai4curation/ai-gene-review ai4curation.github.io Demonstration of AI review of existing functional annotations | 24 | Claude Code, Codex, GitHub Copilot, OpenCode | 22 | 6,891 tok |
| synapseq-foundation/synapseq synapseq.org SynapSeq - Text-Driven Audio Sequencer for Brainwave Entrainment | 24 | Codex, OpenCode | 4 | 1,800 tok |
| tianbing1230/CFPS-Panel-Data-Cleaning-Pipeline CFPS panel data cleaning workflow, with extensive cross-wave harmonization and imputation | 24 | Claude Code, Codex, OpenCode | 2 | 1,965 tok |
| awslabs/llm-evaluation-system Agentic AI-guided evaluation system for comparing LLMs with multi-judge jury scoring | 23 | Claude Code, Codex, OpenCode | 5 | 7,551 tok |
| K-Dense-AI/rowan-autosearch k-dense.ai Agent-driven molecular optimization over chemical space, using Rowan for property scoring | 23 | Codex, OpenCode | 1 | 1,763 tok |
| llorracc/SolvingMicroDSOPs Christopher Carroll's Lecture Notes on Solving Microeconomic Dynamic Stochastic Optimizati | 22 | Claude Code, Codex, OpenCode | 2 | 1,794 tok |
| EthereumPhone/PQ1 | 22 | Claude Code, Codex, OpenCode | 3 | 15,994 tok |
| cpuguy96/StepCOVNet Deep Learning to Create StepMania SM FIles | 22 | Claude Code, Codex, Cursor, OpenCode | 12 | 1,611 tok |
| simple-agent-lab/AutoTrainess simpleagentlab.com Repo for "AutoTrainess: Teaching Language Models to Improve Language Models Autonomously" | 21 | Codex, OpenCode | 1 | 1,265 tok |
| mohsenhariri/scorio mohsenhariri.github.io Bayes@N [ICLR'26], Ranking LLMs [ACL'26 Main]: Statistical evaluation, comparison, and ran | 21 | Claude Code, Codex, OpenCode | 2 | 4,044 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 |
| 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 |
| nickzren/opentargets-mcp MCP server for Open Targets data | 19 | Claude Code, Codex, OpenCode | 2 | 680 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 |
| 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 |
| 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 |