synthetic-sciences/openscience

Profil synthetic-sciences

Dernière activité source enregistrée: 8 octobre 2026 à 10:38

Catalogue SkillsMP mis à jour: 17 octobre 2026 à 00:09

skills collectés: 373

Étoiles GitHub: 4 004
Forks GitHub: 526

README du dépôt

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<div align="center"> <img src="assets/wordmark.svg" alt="OpenScience" width="420"> <br/> <br/> **The open-source AI workbench for scientific research.** Give it a goal. It reads the literature, writes and runs the code, runs the experiments, and writes up what it found, with every step on the record. <br/> [![CI](https://github.com/synthetic-sciences/OpenScience/actions/workflows/ci.yml/badge.svg)](https://github.com/synthetic-sciences/OpenScience/actions/workflows/ci.yml) [![npm](https://img.shields.io/npm/v/%40synsci%2Fopenscience?label=npm&color=1f1f1f)](https://www.npmjs.com/package/@synsci/openscience) [![release](https://img.shields.io/github/v/release/synthetic-sciences/OpenScience?label=release&color=1f1f1f)](https://github.com/synthetic-sciences/OpenScience/releases/latest) [![license](https://img.shields.io/badge/license-Apache%202.0-1f1f1f.svg)](LICENSE) [Download](https://openscience.sh/download) · [Quickstart](https://openscience.sh/docs/#/openscience/quickstart) · [Documentation](https://openscience.sh/docs) · [Changelog](CHANGELOG.md) · [Contributing](CONTRIBUTING.md) <br/> <img src="assets/workspace.png" alt="An OpenScience session comparing EGFR inhibitor potency: the trace shows the search, the written files, the analysis run and the answer with a results table" width="920"> </div> <br/> ## What it is OpenScience is a research agent with a workbench around it. You describe the task in plain language; it plans, gathers evidence, runs code and experiments, and hands back results you can check. It runs as a desktop app, a browser workspace, or a terminal command, on your machine, against your files. It is built for the parts of research that are real work but not the idea: pulling and cleaning data, reproducing a claim, sweeping a parameter, drafting the methods section, checking a reference. You keep the idea and the judgment. - **Every step is visible.** A turn reads as what happened: what it thought, what it searched, what it ran, what it wrote, then the answer. Nothing runs that you cannot see afterwards. - **Real tools, real files.** Shell, Python and R kernels, notebooks, a file system with explicit read and write grants, remote compute when a laptop is not enough. - **Scientific reach.** Hundreds of bundled skills across biology, chemistry, physics, ML and data engineering, plus connectors to databases such as ChEMBL, UniProt, PubMed and arXiv. - **Delegation when it helps.** The lead agent can hand bounded work to workers, in parallel, and keeps the synthesis and the final say. - **Your model, your terms.** Bring your own API keys, sign in to a supported provider, run a local model, or use Ace, the managed pay-as-you-go option. ## Install **Desktop app.** [Download](https://openscience.sh/download) for macOS, Windows or Linux. It updates itself. **Command line and browser workspace.** ```bash npm install -g @synsci/openscience openscience ``` Or run it without installing: ```bash npx synsci ``` Or with the standalone installer on macOS and Linux: ```bash curl -fsSL https://openscience.sh/install | bash ``` Then open **Customize → Models** and connect a provider, or from the terminal: ```bash openscience keys add # your own API key openscience local add # Ollama, LM Studio, or another local endpoint ``` The [installation guide](https://openscience.sh/docs/#/openscience/installation) covers platform details, updates and uninstalling. ## First task Open a project folder and describe the work: ```bash openscience ~/research/my-project ``` ```text Inspect data/samples.csv for missing values and inconsistent labels. Keep the original data unchanged. Save a quality report and a plot in results/, with the code needed to reproduce them. ``` Start with `/plan` when you want to agree on the method first. For a single turn from a script or a pipeline: ```bash openscience run "Review the analysis plan in this project" openscience run --continue "Suggest checks for the assumptions you identified" ``` Review sources, assumptions, code and outputs before relying on a scientific conclusion. The agent shows you what it did so that you can. ## What you can do | Task | What happens | | ------------------------- | ------------------------------------------------------------------------------------------------------------------------------ | | **Review literature** | Search scientific sources, compare findings, save cited evidence. | | **Analyze data** | Inspect inputs, write and run analysis code, produce figures and reports. | | **Reproduce experiments** | Agree on a claim, prerequisites and budget, then compare measured results. | | **Run compute** | Local kernels for everyday work; Modal, SSH hosts, or Slurm and PBS clusters for GPUs and long jobs, approved before they run. | | **Reuse procedures** | Browse the bundled skills or add a workflow specific to your lab. | | **Extend it** | MCP servers, custom agents and commands, plugins, or the TypeScript SDK. | A skill describes a procedure; it does not mean every tool or service it references is installed. Check availability in **Customize** before a substantial task. ### NVIDIA BioNeMo OpenScience ships ten bring-your-own-key adapters for NVIDIA BioNeMo NIM endpoints: Boltz-2, DiffDock, Evo 2, GenMol, MolMIM, MSA Search, OpenFold2, OpenFold3, ProteinMPNN and RFdiffusion. Each has a strict request schema, one approval per dispatch, and hashed artifacts written into the session; they are marked experimental and need your own NVIDIA API key under NVIDIA's service terms. The `protein-binder-design` skill is adapted from the [NVIDIA BioNeMo Agent Toolkit](https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit) (CC-BY-4.0 skills, Apache-2.0 code), pinned at commit `0e67a61`. See [Scientific tools](https://openscience.sh/docs/#/openscience/tool-catalog) and [Service credentials](https://openscience.sh/docs/#/openscience/service-credentials). ## How it works ```text your request → Research agent plans, then works step by step → tools: shell, Python/R kernels, files, search, connectors, compute → workers for bounded parallel tasks (explore, general, and five domain specialists) → answer, with the trace and the files it produced ``` - **Permissions.** Choose how much to ask: always, only for risky actions, or full access. Network commands ask once per destination host. Files outside the project are read or written only with an explicit grant. - **Working folder.** A conversation works in the project's connected folder; caches and throwaway output stay in a per-session scratch space. - **Publishing stays with you.** `git push`, releases and uploads run from the lead session with this machine's own GitHub and Hugging Face logins; no token is ever asked for in chat. The [capability map](https://openscience.sh/docs/#/openscience/capabilities), [Explore tools](https://openscience.sh/docs/#/openscience/explore-tools) and the [skills directory](https://openscience.sh/docs/#/openscience/skill-library) list what is available and how to set it up. ## Benchmarks | Benchmark | OpenScience | | --------------------------------------------- | ------------: | | Terminal-Bench Science (70 tasks) | 53/70 (75.7) | | BiomniBench-DA (public 50) | 82.2 | | Terminal-Bench 4.0, science subset (14 tasks) | 0.714 (10/14) | GPT-6 Astra and GPT-6 Sol on Harbor, with each benchmark's native environments, verifiers and judge. The results, with the trace of every counted trial, are in [benchmarks-openscience](https://github.com/synthetic-sciences/benchmarks-openscience). ## Model access | Option | Setup | Cost | | ----------------- | --------------------------------------------- | ------------------------------------------------------ | | **Your provider** | An API key or a supported sign-in. | Your provider's billing. | | **Local model** | Ollama, LM Studio or any compatible endpoint. | Your hardware. | | **Ace** | Sign in, choose a workspace, fund its Wallet. | Pay as you go at the Wallet rate shown for each model. | Ace has no subscription. Direct provider routes add no fee; models served through OpenRouter include its funding fee (5.5% by default), already counted in the displayed rate. The card processing fee is shown at checkout. First-run setup asks you to sign in to an OpenScience account; headless `openscience run` does not. Model usage through your own keys or a local model is never charged to an Ace Wallet. Details are in [Models](https://openscience.sh/docs/#/openscience/models), [Local models](https://openscience.sh/docs/#/openscience/local-models) and [Pricing](https://openscience.sh/docs/#/openscience/pricing). ## Documentation | Topic | Guides | | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | First use | [Quickstart](https://openscience.sh/docs/#/openscience/quickstart), [Workspace](https://openscience.sh/docs/#/openscience/workspace), [Workflow cookbook](https://openscience.sh/docs/#/openscience/workflow-examples) | | Research | [Literature reviews](https://openscience.sh/docs/#/openscience/literature-review), [Data analysis](https://openscience.sh/docs/#/openscience/data-analysis), [Reproduction](https://openscience.sh/docs/#/openscience/reproduction), [Writing](https://openscience.sh/docs/#/openscience/writing) | | Capabilities | [Skills](https://openscience.sh/docs/#/openscience/skill-library), [Databases](https://openscience.sh/docs/#/openscience/databases), [Connectors](https://openscience.sh/docs/#/openscience/connectors) | | Control | [Permissions](https://openscience.sh/docs/#/openscience/permissions), [Files](https://openscience.sh/docs/#/openscience/files), [Project instructions](https://openscience.sh/docs/#/openscience/instructions), [Configuration](https://openscience.sh/docs/#/openscience/configuration) | | Automate | [CLI reference](https://openscience.sh/docs/#/openscience/commands), [JSON output](https://openscience.sh/docs/#/openscience/automation), [SDK and editors](https://openscience.sh/docs/#/openscience/extensions) | | Help | [Troubleshooting](https://openscience.sh/docs/#/openscience/troubleshooting), [FAQ](https://openscience.sh/docs/#/openscience/faq) | The documentation is also available as plain text for agents: [llms.txt](https://openscience.sh/docs/llms.txt) and [llms-full.txt](https://openscience.sh/docs/llms-full.txt). ## Repository ```text backend/cli The openscience CLI and local server: sessions, tools, providers, skills frontend/workspace The browser workspace (SolidJS), embedded into the CLI at build time frontend/ui Shared components, themes and icons frontend/desktop The Electron shell and its signed self-updater frontend/docs The documentation site tooling/sdk The TypeScript SDK, generated from the server's OpenAPI contract tooling/plugin The plugin runtime docs/notes Engineering notes: verification, releases, how to add a skill, tool or connector ``` ```bash bun run setup # verify Bun, install, embed the workspace UI bun dev # run from source bun run check # format, typecheck and every unit suite ``` [ARCHITECTURE.md](ARCHITECTURE.md) explains how the pieces fit. [CONTRIBUTING.md](CONTRIBUTING.md) has the development loops, the checks that gate a pull request, and how to add a skill, connector, tool or plugin. [AGENTS.md](AGENTS.md) holds the conventions the code follows. ## Releases Stable releases are cut from `main` by the publish workflow after a full rehearsal at the same commit: packaged end-to-end tests, operating-system smokes and scientific capability canaries on every native platform. [GitHub Releases](https://github.com/synthetic-sciences/OpenScience/releases) carries the desktop installers, CLI archives and checksums; the [changelog](CHANGELOG.md) records what changed for users. The desktop app updates itself. For the CLI, run `openscience upgrade`, or `npm install -g @synsci/openscience@latest` for an npm installation. ## Community and support - Bugs and feature requests: [GitHub Issues](https://github.com/synthetic-sciences/OpenScience/issues). Use the templates; a good report has a reproduction. - Security: [SECURITY.md](SECURITY.md). Please report vulnerabilities privately. - Conduct: [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md). - Billing and account questions: use the account support channel rather than a public issue. ## Acknowledgements OpenScience is inspired by [OpenCode](https://opencode.ai) by [Anomaly](https://github.com/anomalyco/opencode) and shares its commitment to excellent open-source agents. We want to bring strong, open-source scientific agents to everyone. Most of the bundled skills come from open collections written by other people: - [Scientific Agent Skills](https://github.com/K-Dense-AI/scientific-agent-skills) and [Claude Scientific Writer](https://github.com/K-Dense-AI/claude-scientific-writer) by **K-Dense Inc.** (MIT) — 180 of the biology, chemistry, database, research, writing and visualization skills. If they contribute to published work, cite Kassis, Agarwal, He, Patel and Brueckner, [_Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents_](https://arxiv.org/abs/2609.00065) (2026). - [AI Research Skills](https://github.com/Orchestra-Research/AI-Research-SKILLs) by **Orchestra Research** (MIT) — 79 of the ML training, inference, LLM-tooling and cloud-compute skills. - [Hugging Face skills](https://github.com/huggingface/skills) by **Hugging Face** (Apache-2.0) — the `hugging-face-*` skills. - [Anthropic's document skills](https://github.com/anthropics/skills) (docx, pdf, pptx, xlsx), under Anthropic's terms. - [NVIDIA BioNeMo Agent Toolkit](https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit) (CC-BY-4.0 / Apache-2.0) — the protein binder design workflow. - [MarkItDown](https://github.com/microsoft/markitdown) by Microsoft (MIT), [Claude-Science-System-Prompts](https://github.com/Shoko-official/Claude-Science-System-Prompts) by Shoko-official (Apache-2.0), [pacsomatic](backend/cli/skills/biology/pacsomatic) by Beifang Niu (MIT), and [Iconoir](https://github.com/iconoir-icons/iconoir) icons (MIT). [`backend/cli/skills/ATTRIBUTION.md`](backend/cli/skills/ATTRIBUTION.md) lists every derived skill with its upstream path and license, and each skill's frontmatter names its original author. [NOTICE](NOTICE) carries the license texts. ## License Apache License 2.0. See [LICENSE](LICENSE) and [NOTICE](NOTICE). OpenScience is an independent project. It is not affiliated with, endorsed by, or sponsored by any model provider. Provider and model names are used only to describe compatibility.

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neuropixels-analysis

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Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when…