Scientific Agent Skills

Install

npx skills add K-Dense-AI/scientific-agent-skills

This is third-party code. Review the repository files before installing.

What it does

A collection of Agent Skills that gives an agent curated workflows for scientific Python packages and databases. It includes skills for RDKit, Scanpy, BioPython, PyTorch Lightning, Qiskit and pymatgen, a unified database-lookup skill for 78 public databases (PubChem, UniProt, ClinicalTrials.gov and others), and integrations such as Benchling, Opentrons and LabArchives. Every skill that ships scripts has a test suite in CI.

Who it is for. Scientists, bioinformaticians, data analysts and labs that use an agent for research computing.

Example request

Load my h5ad file, run QC and cell clustering in Scanpy and plot a UMAP

Limitations

The authors warn that skills can run code, install packages and make network requests, and community contributions may be less thoroughly reviewed. Installing the full collection adds a lot of standing context, so a topical subset is recommended. Requires Python and uv; Windows only via WSL2. Clinical skills are for research, not patient decisions.

How to disable. Remove unneeded skill folders from your agent's skills directory or disable the plugin in your client. If you used gh skill, manage installed skills through gh skill.

Security check

• Skills run Python scripts and install packages via uv
• They call external APIs and scientific databases
• Some community skills are not exhaustively reviewed

README in short

Scientific Agent Skills (formerly Claude Scientific Skills) is K-Dense's collection of 166 skills for scientific and research tasks. They span genomics, drug discovery, proteomics, clinical research, medical imaging, materials science, astronomy, geospatial work and scientific communication. The repository is also an Agent Plugins package. Install via npx skills, gh skill, Cursor or Codex plugins, or a manual clone. The project is described in arXiv:2609.00065 and includes a dedicated security section.

SKILL.md

---
name: biopython
description: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
allowed-tools: Read Write Edit Bash
compatibility: Requires Python 3.10+, NumPy, and Biopython. Entrez and web BLAST examples require network access; local BLAST/MUSCLE examples require those command-line tools installed separately.
license: Biopython License Agreement
metadata:
  version: "1.3"
  skill-author: K-Dense Inc.
  openclaw:
    envVars:
    - name: NCBI_EMAIL
      required: false
      description: Email for NCBI Entrez identification (required by NCBI policy for Entrez calls).
    - name: NCBI_API_KEY
      required: false
      description: NCBI API key to raise Entrez rate limits.
---

# Biopython: Computational Molecular Biology in Python

## Overview

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is **Biopython 1.87** (released 30 March 2026). It supports **Python 3.10-3.14** and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses **CVE-2025-68463** in `Bio.Entrez.Parser` when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML.

## When to Use This Skill

Use this skill when:

- Working with biological sequences (DNA, RNA, or protein)
- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
- Running BLAST searches or parsing BLAST results
- Performing sequence alignments (pairwise or multiple sequence alignments)
- Analyzing protein structures from PDB files
- Creating, manipulating, or visualizing phylogenetic trees
- Finding sequence motifs or analyzing motif patterns
- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
- Performing structural bioinformatics tasks
- Working with population genetics data
- Any other computational molecular biology task

## Core Capabilities

Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:

1. **Sequence Handling** - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
2. **Alignment Analysis** - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
3. **Database Access** - Bio.Entrez for programmatic access to NCBI databases
4. **BLAST Operations** - Bio.Blast for running and parsing BLAST searches
5. **Structural Bioinformatics** - Bio.PDB for working with 3D protein structures
6. **Phylogenetics** - Bio.Phylo for phylogenetic tree manipulation and visualization
7. **Advanced Features** - Motifs, population genetics, sequence utilities, and more

## Installation and Setup

Install the current stable Biopython release with an explicit version pin for reproducibility:

```bash
uv pip install "biopython==1.87"

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