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What you can do with Scientific Agent Skills

A library of 177 Agent Skills that give AI agents documented, validated guidance for scientific packages, databases, and research workflows.

#5 in this week's top 10 trending AI repos

K-Dense-AI/scientific-agent-skills on GitHub

Third-party repos we don't own or vouch for. AI-generated use cases can be wrong: review everything and run at your own risk.

What do you want to do?

4 use cases

  • Pull compound and protein records with source provenance

    Query public biology and chemistry databases and get each record with its source endpoint.

    View prompt
    Using the scientific-agent-skills repo, read skills/database-lookup/SKILL.md and query PubChem, ChEMBL, and UniProt for <target gene or compound list>. Return a table of identifiers and key properties, with the endpoint and access date for each row. Verify that every row names its source endpoint and flag any database that needs a key you do not have.

  • Screen a compound list for drug-like properties

    Use RDKit-based skills to predict molecular properties and flag ADMET concerns in a candidate set.

    View prompt
    Using the scientific-agent-skills repo and its RDKit cheminformatics skill, compute molecular properties and ADMET flags for the SMILES in <file of SMILES strings>. Return a ranked table with the computed values and the code used. Verify that every input structure parses and that no row is silently dropped.

  • Run a single-cell RNA-seq analysis with Scanpy

    Have an agent follow the Scanpy skill to process a single-cell dataset and report clusters.

    View prompt
    Using the scientific-agent-skills repo and its Scanpy single-cell skill, process the dataset at <dataset path> with quality control, clustering, and a cluster summary. Return a script and a short report of cell counts per cluster. Verify the cell and gene counts before and after filtering.

  • Draft a literature review with traceable citations

    Synthesize papers on a topic and keep each claim linked to a citable source.

    View prompt
    Using the scientific-agent-skills repo and its evidence-traceable writing and literature synthesis skills, write a literature review on <topic> from the papers listed in <paper list>. Return a draft with a citation after each claim and a matching bibliography. Verify that every cited claim appears in the named source.

How to use Scientific Agent Skills

  1. Check you have what it needs: An agent host that supports Agent Skills, such as Claude Code, Cursor, or Codex; Git, to clone the repository (inferred); Python, since the repository language is Python.
  2. Open K-Dense-AI/scientific-agent-skills on GitHub and read the README and license.
  3. git clone https://github.com/K-Dense-AI/scientific-agent-skills (inferred, check the README)
  4. Follow the install steps in the Getting Started section of the README for your agent host.
  5. Open skills/database-lookup/SKILL.md, which documents 80 databases with endpoint selection, pagination, and provenance.
  6. Give your agent the target list and the databases to query, such as PubChem, ChEMBL, or UniProt.

These steps come from our top use case, Pull compound and protein records with source provenance, which also has a copy-paste agent prompt.

Scientific Agent Skills alternatives · Best AI repos for Research

About this repo

Requirements

  • An agent host that supports Agent Skills, such as Claude Code, Cursor, or Codex
  • Git, to clone the repository (inferred)
  • Python, since the repository language is Python
  • API keys or accounts for any registered or licensed database you plan to query
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Questions about Scientific Agent Skills

What is Scientific Agent Skills?

A library of 177 Agent Skills that give AI agents documented, validated guidance for scientific packages, databases, and research workflows. It is an open-source project on GitHub: https://github.com/K-Dense-AI/scientific-agent-skills.

Who is Scientific Agent Skills for?

Scientists, lab staff, and developers who want an AI coding agent to handle science tasks using curated skill documentation.

What can I do with Scientific Agent Skills?

4 use cases so far, for example: Pull compound and protein records with source provenance; Screen a compound list for drug-like properties; Run a single-cell RNA-seq analysis with Scanpy. Each has steps and a copy-paste agent prompt.

What do I need to run Scientific Agent Skills?

An agent host that supports Agent Skills, such as Claude Code, Cursor, or Codex; Git, to clone the repository (inferred); Python, since the repository language is Python; API keys or accounts for any registered or licensed database you plan to query.

What are alternatives to Scientific Agent Skills?

Other hot AI repos in Research: Speaker Mem R1, DSH Council, Evo Bot, AI Engineering Course, AI System Design.

Is Scientific Agent Skills safe to run?

Deduped does not own, audit or vouch for it. Read the README and license, run it on your own systems first and review every command before you run it.