bioinformatics-agent-skills

# bioinformatics-agent-skills

Gives an AI coding agent expert skills for computational biology, from RNA-seq and single-cell analysis to protein structure, molecular dynamics, peptide design, literature mining and publication figures.

Made by ssinder on GitHub. These notes are Mindket's, written from its README; the project's own files and license are in its repository.

## About

What it is: bioinformatics-agent-skills is a curated set of agent skills for computational biology. Each skill is a SKILL.md package that gives your coding agent subject knowledge, repeatable workflows and checks on the results, so it does more than call an API.

Who it suits: It suits researchers who already work in computational biology and want an AI coding agent that knows the field's standard analyses.

```table
Industry | Who uses it | How they use it | Example
Academic research | Computational biologists | Ask an agent to run analysis workflows on RNA-seq or single-cell data | Analyzing transcriptomic data from an experiment
Biotech | Protein and peptide designers | Use the structure, docking and peptide design skills | Designing antimicrobial peptides
Research labs | Analysts who support other scientists | Reuse the same workflows and validation checks across projects | Re-running an analysis the same way each time
Scientific publishing | Researchers preparing papers | Use the publication-grade figures skill | Making figures for a manuscript
```

You can skip it if your work is outside computational biology, since every skill in it is built for that field.

Where to use it: Use it in any of these agents.

- Claude Code
- Cursor
- Codex
- Any host that supports the open Agent Skills standard

```table
Use case | Who | What they get back
Transcriptomics and single-cell analysis | Biologists with expression data | Skills that bring subject knowledge, workflows and result checks to the analysis
Protein structure and dynamics | Structural biologists | Skills for structure work, docking, molecular dynamics and inter-chain contact analysis with PyMOL visualization
Peptide design | Peptide researchers | Skills for antimicrobial peptide design and machine learning peptide generation
Literature mining and figures | Any researcher | Help with NCBI BioProject metadata and publication-grade figures
```

How to set it up: You need two things before you start.

- An agent host that supports the open Agent Skills standard, such as Claude Code, Cursor or Codex
- A copy of the project's code from its GitHub page

1. Download the project's code from its GitHub page.
2. Follow the setup in its README to put the skills where your agent loads them.

Example: You ask your agent for help with a single-cell analysis of your data. The agent picks the matching skill and works from its workflow and checks instead of writing the analysis from scratch.

For newcomers and experts: An agent skill is a folder with a SKILL.md file that your agent reads when a task fits it. Your first small try is to pick the area you work in, such as RNA-seq, and ask your agent for one routine step in it.

The library was rebuilt from 217 research scripts that sat in a private archive, and it now follows an open standard. The migration map lists, script by script, which parts were carried over and which were redone, with reasons. Coverage is limited to the areas listed above.

```flow
Your request matches a skill
The agent reads that skill's SKILL.md
It follows the workflow in the skill
It runs the skill's validation checks
```

Good to know:

- License: MIT
- The project has full documentation with a quick start, a skill catalogue, methodology references and troubleshooting
- Nothing in this kit runs by itself

## On GitHub, 8 November 2026

- Stars: 75
- Forks: 6
- Open issues and pull requests: 0
- Language: Python
- License: MIT
- Topics: agent-skills, agent-skills-standard, bioinformatics, claude-code, claude-skills, computational-biology, literature-mining, molecular-dynamics, peptide-design, protein-structure, research-tools, rna-seq

## Links

- Code: https://github.com/ssinder/bioinformatics-agent-skills
- Website: https://ssinder.github.io/bioinformatics-agent-skills/
- Releases: https://github.com/ssinder/bioinformatics-agent-skills/releases
- Issues: https://github.com/ssinder/bioinformatics-agent-skills/issues
- Star history: https://www.star-history.com/#ssinder/bioinformatics-agent-skills&Date

## Get the code

```
git clone https://github.com/ssinder/bioinformatics-agent-skills.git
```

Then follow the setup in its README. Nothing in this kit runs by itself.

README.md  4 KB