How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.
biopython
biopython is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “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 bioinformati…”. The project has 34k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/biopython`.
What biopython does
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.
Installation
Add biopython to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/biopythonAlways review a skill's source before installing it. This command comes from the skill's public repository; the linked repo is the source of truth for exact setup steps.
What's inside
The SKILL.md for biopython is organised into these sections:
- Overview
- When to Use This Skill
- Core Capabilities
- Installation and Setup
- Using This Skill
- 1. Sequence Handling (Bio.Seq & Bio.SeqIO)
- 2. Alignment Analysis (Bio.Align & Bio.AlignIO)
- 3. Database Access (Bio.Entrez)
- 4. BLAST Operations (Bio.Blast)
- 5. Structural Bioinformatics (Bio.PDB)
- 6. Phylogenetics (Bio.Phylo)
- 7. Advanced Features
When to use it
Reach for biopython when you want data help from your agent without writing the same instructions every session. Load the skill and the agent picks it up automatically for relevant tasks.
Strengths
- Clear MIT license — safe to read and adapt
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 33,821 GitHub stars
- Actively maintained (recent commits)
Topics
Frequently asked questions
- What does biopython do?
- 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.
- How do I install biopython?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/biopython in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is biopython free to use?
- Yes. biopython is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does biopython come from?
- biopython ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 41 catalogued skills in total. The repository's 33,821 GitHub stars apply to that whole collection, not to this skill on its own.
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