biopython SKILL.md skillA
biopython from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/biopython@v1.5Pins v1.5 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/biopython/SKILL.md- Versions recorded
- 7
- Latest version
- v1.5, committed Oct 1, 2026
- First version recorded
- Jun 11, 2026
- Size
- 17,223 bytes
- Repository stars
- 53,159
- License
- MIT
Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-biology pipelines, BLAST automation, structure analysis, and motif analysis.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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. These examples target **Biopython 1.88** (released 6 August 2026), tested here on Python 3.13. It requires Python 3.10+ and NumPy; Python 3.10 support is deprecated. Upgrade to 1.88 for its `Bio.Nexus` parser security fix, in addition to the Entrez XML fix in 1.87. See the [release notes](https://github.com/biopython/biopython/blob/biopython-188/NEWS.rst). Local example checks and external-service limits are recorded in `references/review.md`; examples requiring user files or external programs are illustrative unless listed there as exercised. ## 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 …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/biopython@sha256:b617561b38a2e3ecThe line at the top of this page pins the label v1.5, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_tp66uvgxxggstmpi)
5 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 7 versions of this file, between Jun 11, 2026 and Oct 1, 2026, about one every 19 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.5 latest | 2026-10-01 | a92663a | 17,223 B | A | view · diff |
| v1.4 | 2026-09-30 | ce9e6e9 | 17,234 B | A | view · diff |
| v1.3 | 2026-09-02 | 1e5eeff | 17,046 B | A | view · diff |
| v1.2 | 2026-07-26 | b085e11 | 16,089 B | A | view · diff |
| git:20260611.c1150bd | 2026-06-11 | c1150bd | 16,396 B | A | view · diff |
| git:20260611.fe3f715 | 2026-06-11 | fe3f715 | 16,090 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 15,816 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (17223 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 53,159 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_tp66uvgxxggstmpi GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/biopython GET https://markdownregistry.com/api/v1/blob/b617561b38a2e3ecc8f8cf3dd8bb0307ac1aaf4d67e6e0432b0c248bc4382245
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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