[Upstream sync] K-Dense-AI/scientific-agent-skills (github) — 0 added, 137 modified #62
@@ -2,9 +2,9 @@
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title: "Scientific Agent Skills"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/390f5146/README.md
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upstream_sha: 390f5146
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imported_at: 2026-08-20
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffb/README.md
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upstream_sha: 1e5eeffb
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imported_at: 2026-09-02
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prompt_class: catalogue
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upstream_changes: accepted
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author: upstream
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@@ -14,7 +14,8 @@ validated: false
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# Scientific Agent Skills
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[](LICENSE.md)
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[](pyproject.toml)
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[](https://arxiv.org/abs/2609.00065)
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[](pyproject.toml)
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[](#-whats-included)
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[](#-whats-included)
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[](https://agentskills.io/)
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@@ -29,13 +30,15 @@ validated: false
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> **🔔 Claude Scientific Skills is now Scientific Agent Skills.** Same skills, broader compatibility — now works with any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, not just Claude.
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> **New: [K-Dense BYOK](https://github.com/K-Dense-AI/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 161 skills in this repo. Your data stays on your computer, and you can optionally scale to cloud compute via [Modal](https://modal.com/) for heavy workloads. [Get started here.](https://github.com/K-Dense-AI/k-dense-byok)
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> **New: [K-Dense BYOK](https://github.com/K-Dense-AI/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](https://modal.com/) for heavy workloads. [Get started here.](https://github.com/K-Dense-AI/k-dense-byok)
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> **🎥 Live webinar — [Getting Started with K-Dense BYOK](https://luma.com/nucztxt5)** · Tuesday, August 25, 2026 · 2:00 PM PT / 5:00 PM ET · Online, free
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> Join us for a hands-on walkthrough of [K-Dense BYOK](https://github.com/K-Dense-AI/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'll show you how to set it up, bring your own API keys, and run real research workflows with these skills. No prior technical experience needed, and questions are welcome throughout. **[Save your spot →](https://luma.com/nucztxt5)**
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> **🎥 Webinar recording — [Getting Started with K-Dense BYOK](https://youtu.be/Du3BIE48DKc?si=9dPpETKSc2PeQbvU)**
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> A hands-on walkthrough of [K-Dense BYOK](https://github.com/K-Dense-AI/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 →](https://youtu.be/Du3BIE48DKc?si=9dPpETKSc2PeQbvU)**
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> **Stay up to date:** Follow K-Dense on [X](https://x.com/k_dense_ai), [LinkedIn](https://www.linkedin.com/company/k-dense-inc), [YouTube](https://www.youtube.com/@K-Dense-Inc), and [Reddit](https://www.reddit.com/user/-k-dense-/) for new skills, release announcements, walkthroughs, research workflow demos, and examples you can use with your own AI agent.
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> **📄 Paper:** Scientific Agent Skills is described in [*Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents*](https://arxiv.org/abs/2609.00065) (arXiv:2609.00065). If you use these skills in your research, please [cite the paper](#-citation).
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A comprehensive collection of **163 ready-to-use scientific and research skills** (covering cancer genomics, individual-level 1000 Genomes queries, hosted regulatory-sequence prediction, live pathogen-variant surveillance, analytical method validation, PK/PD modelling and dose selection, full-text biomedical and regulatory literature retrieval, drug-target binding, bounded biomedical knowledge graph search, molecular dynamics, RNA velocity, microbiome foundation models, geospatial science, time series forecasting, scientific ML resource discovery via Hugging Science, 78+ scientific databases, and more) for any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, created by [K-Dense](https://k-dense.ai). The repository is also a portable [Agent Plugins](https://agent-plugins.org/) package (`plugin.json` + `skills/`), so plugin-capable clients can load the whole collection as one plugin. Works with **Cursor, Claude Code, Codex, Google Antigravity, and more**. Transform your AI agent into a research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
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> ⭐ **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](https://github.com/K-Dense-AI/scientific-agent-skills). 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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@@ -48,6 +51,7 @@ These skills enable your AI agent to seamlessly work with specialized scientific
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- 🔬 Proteomics & Mass Spectrometry - LC-MS/MS processing, peptide identification, spectral matching, protein quantification
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- 🏥 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
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- 🧠 Healthcare AI & Biosignal Research - EHR and model research, physiological signal analysis, and retrospective validation—not patient-specific diagnosis, treatment, alarms, or deployment decisions
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- 🐭 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
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- 🖼️ Medical Imaging & Digital Pathology - Privacy-aware DICOM processing and research-only whole-slide image analysis, computational pathology, and radiology data workflows
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- 🤖 Machine Learning & AI - Deep learning, reinforcement learning, time series analysis, model interpretability, Bayesian methods
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- 🔮 Materials Science & Chemistry - Crystal structure analysis, phase diagrams, metabolic modeling, computational chemistry
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@@ -130,7 +134,7 @@ Each skill includes:
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- **Multi-Step Workflows** - Execute complex pipelines with a single prompt
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### 🎯 **Comprehensive Coverage**
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- **161 Skills** - Extensive coverage across all major scientific domains
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- **163 Skills** - Extensive coverage across all major scientific domains
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- **100+ Databases** - Unified access to 78+ databases via database-lookup, plus dedicated data access skills and multi-database packages like BioServices, BioPython, and gget
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- **70+ Optimized Python Package Skills** - Current, version-scoped guidance for packages including RDKit, Scanpy, PyTorch Lightning, scikit-learn, PyTDC, pydicom, PufferLib, QuTiP, GeoPandas, pymatgen, Qiskit, Molecular Dynamics (OpenMM/MDAnalysis), scVelo, and TimesFM (the agent can use any Python package; these are the pre-documented paths)
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@@ -185,7 +189,7 @@ Pin to a specific release tag or commit SHA for reproducible installs:
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```bash
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# Pin to a release tag
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gh skill install K-Dense-AI/scientific-agent-skills --pin v2.64.0
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gh skill install K-Dense-AI/scientific-agent-skills --pin v2.65.0
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# Pin to a commit SHA
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gh skill install K-Dense-AI/scientific-agent-skills --pin abc123def
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@@ -237,7 +241,7 @@ For Hermes versions that support skill taps, add the repository as a tap:
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hermes skills tap add K-Dense-AI/scientific-agent-skills
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```
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Every `SKILL.md` has YAML frontmatter, but legacy and community skills vary in `metadata` formatting (block or flow style) and optional extension fields. Repository updates must keep `metadata.version` as a quoted numeric string and pass canonical `skills-ref validate ./skills/<skill-name>` checks. Hosts may interpret optional metadata and credential prompts differently, so verify behavior on the target host. Because 161 skills add up to a lot of standing context, consider installing a topical subset rather than the whole collection.
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Every `SKILL.md` has YAML frontmatter, but legacy and community skills vary in `metadata` formatting (block or flow style) and optional extension fields. Repository updates must keep `metadata.version` as a quoted numeric string and pass canonical `skills-ref validate ./skills/<skill-name>` checks. Hosts may interpret optional metadata and credential prompts differently, so verify behavior on the target host. Because 163 skills add up to a lot of standing context, consider installing a topical subset rather than the whole collection.
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> **NemoClaw note:** NemoClaw runs agents inside NVIDIA OpenShell with default-deny outbound networking. Skills are discovered and loaded normally, but any skill that needs the network — package installs via `uv`, or API calls (Exa, Parallel, Benchling, NCBI, Materials Project, …) — only works once the operator pre-approves the relevant domains in the OpenShell TUI.
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@@ -515,6 +519,9 @@ This repository contains **163 scientific and research skills** organized across
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- Decision-support research: local, aggregate or synthetic Clinical Decision Support evaluation and governance artifacts only
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- Clinical documentation: source-bound Clinical Reports drafts and formatting of verified clinician-authored decisions with Treatment Plans; neither skill diagnoses or recommends care
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#### 🐭 **Preclinical Research & Animal Welfare** (1 skill)
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- Severity assessment: RELSA Severity Assessment (multivariate RELSA scores from body weight, temperature, clinical/nesting scores, biomarkers, activity, heart rate, burrowing and wheel running; ARIMA humane-endpoint forecasting with 95% prediction intervals; KDE-derived attention and danger zones for 3Rs/refinement and EU Directive 2010/63/EU severity reporting) — an aid to severity assessment, never a decision rule
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#### 🖼️ **Medical Imaging & Digital Pathology** (4 skills)
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- DICOM processing: pydicom 3.0.2 with privacy-first local preflight and no diagnostic or de-identification-compliance claims
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- Whole slide imaging: histolab and research-only PathML 3.0.5
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@@ -868,44 +875,65 @@ Need help? Here's how to get support:
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## 📖 Citation
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If you use Scientific Agent Skills in your research or project, please cite the overall collection and, when relevant, the individual skill or skills that materially supported your work.
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If you use Scientific Agent Skills in your research or project, please cite our paper:
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The collection citation helps others find the repository, understand the broader skill ecosystem used in your workflow, and credit the maintenance effort behind Scientific Agent Skills. Individual skill citations give more precise credit for the specific package, database, or workflow guidance your agent used.
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> Timothy Kassis, Vinayak Agarwal, Yuhuan He, Darshil Patel, and Aubrey M. Brueckner. **Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents.** arXiv:2609.00065, 2026. [https://arxiv.org/abs/2609.00065](https://arxiv.org/abs/2609.00065)
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When relevant, also cite the individual skill or skills that materially supported your work.
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GitHub's **Cite this repository** button, backed by [`CITATION.cff`](CITATION.cff), produces the same paper citation in APA or BibTeX.
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The paper citation helps others find the repository, understand the broader skill ecosystem used in your workflow, and credit the maintenance effort behind Scientific Agent Skills. Individual skill citations give more precise credit for the specific package, database, or workflow guidance your agent used.
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Recommended practice:
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- Always cite **Scientific Agent Skills** using one of the formats below.
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- Always cite the **Scientific Agent Skills paper** using one of the formats below.
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- Also cite each individual skill that directly contributed to your analysis, code, figures, reports, or research workflow.
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- If a skill wraps or documents an external package, database, or platform, cite that upstream project too when your field's norms require it.
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### Collection Citation
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### Paper Citation
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#### BibTeX
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```bibtex
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@misc{kassis2026scientificagentskills,
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title = {Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents},
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author = {Kassis, Timothy and Agarwal, Vinayak and He, Yuhuan and Patel, Darshil and Brueckner, Aubrey M.},
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year = {2026},
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eprint = {2609.00065},
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archivePrefix = {arXiv},
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primaryClass = {cs.CL},
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url = {https://arxiv.org/abs/2609.00065}
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}
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```
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#### APA
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```
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Kassis, T., Agarwal, V., He, Y., Patel, D., & Brueckner, A. M. (2026). Scientific Agent Skills: A library of procedural knowledge for research agents. arXiv. https://arxiv.org/abs/2609.00065
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```
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#### MLA
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```
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Kassis, Timothy, et al. "Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents." arXiv, 2026, arxiv.org/abs/2609.00065.
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```
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#### Plain Text
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```
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Kassis, T., Agarwal, V., He, Y., Patel, D., & Brueckner, A. M. (2026). Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents. arXiv:2609.00065. https://arxiv.org/abs/2609.00065
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```
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### Software Citation
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If you also need to cite a specific version of the repository itself (for example, to pin the exact skill set an analysis ran against), add a software citation alongside the paper and record the release tag or commit you used:
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```bibtex
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@software{scientific_agent_skills_2026,
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author = {{K-Dense Inc.}},
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title = {Scientific Agent Skills: A Comprehensive Collection of Scientific Tools for AI Agents},
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year = {2026},
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url = {https://github.com/K-Dense-AI/scientific-agent-skills},
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note = {161 skills covering databases, packages, integrations, and analysis tools}
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note = {163 skills covering databases, packages, integrations, and analysis tools}
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}
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```
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#### APA
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```
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K-Dense Inc. (2026). Scientific Agent Skills: A comprehensive collection of scientific tools for AI agents [Computer software]. https://github.com/K-Dense-AI/scientific-agent-skills
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```
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#### MLA
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```
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K-Dense Inc. Scientific Agent Skills: A Comprehensive Collection of Scientific Tools for AI Agents. 2026, github.com/K-Dense-AI/scientific-agent-skills.
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```
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#### Plain Text
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```
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Scientific Agent Skills by K-Dense Inc. (2026)
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Available at: https://github.com/K-Dense-AI/scientific-agent-skills
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```
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### Individual Skill Citation
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When citing a specific skill, include the skill name, version from `metadata.version` in that skill's `SKILL.md`, and the direct skill URL. For example:
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@@ -949,13 +977,3 @@ See [LICENSE.md](LICENSE.md) for full terms.
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### Individual Skill Licenses
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> ⚠️ **Important**: Each skill has its own license specified in the `license` metadata field within its `SKILL.md` file. These licenses may differ from the repository's MIT License and may include additional terms or restrictions. **Users are responsible for reviewing and adhering to the license terms of each individual skill they use.**
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## Star History
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<a href="https://star-history.dera.page/#K-Dense-AI/scientific-agent-skills">
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<picture>
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<source media="(prefers-color-scheme: dark)" srcset="https://star-history.dera.page/svg?repos=K-Dense-AI/scientific-agent-skills&theme=dark" />
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<source media="(prefers-color-scheme: light)" srcset="https://star-history.dera.page/svg?repos=K-Dense-AI/scientific-agent-skills" />
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<img alt="Star History Chart" src="https://star-history.dera.page/svg?repos=K-Dense-AI/scientific-agent-skills" />
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</picture>
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</a>
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