biopython-molecular-biology SKILL.md skillA
biopython-molecular-biology from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/biopython-molecular-biology@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/biopython-molecular-biology/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 24,218 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
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 Toolkit ## Overview Biopython is the standard open-source Python library for computational molecular biology, providing modular APIs for sequence handling, biological file parsing, NCBI database access, BLAST searches, protein structure analysis, and phylogenetics. It supports Python 3 and requires NumPy. ## When to Use - Parse and convert biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, PHYLIP) - Fetch sequences or publications from NCBI databases (GenBank, PubMed, Protein) programmatically - Run and parse BLAST searches (remote NCBI or local BLAST+) - Perform pairwise or multiple sequence alignments with custom scoring - Analyze 3D protein structures — distances, angles, DSSP, superimposition - Build and visualize phylogenetic trees from sequence alignments - Calculate sequence statistics (GC content, molecular weight, melting temperature) - Batch-process thousands of sequences with custom filtering logic - Use `pysam` instead for reading SAM/BAM/CRAM alignment files and working with mapped reads; use `scikit-bio` instead for advanced ecological diversity metrics ## Prerequisites …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/biopython-molecular-biology@sha256:b7100575f614470dThe line at the top of this page pins the label git:20260428.81ea2d2, 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_eekaojuxvgf7gtnf)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 35 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 24,218 B | A | view · diff |
| git:20260218.2a275f1 | 2026-02-18 | 2a275f1 | 24,360 B | A | view · diff |
| git:20260218.e460066 | 2026-02-18 | e460066 | 23,679 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 (24218 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_eekaojuxvgf7gtnf GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/biopython-molecular-biology GET https://markdownregistry.com/api/v1/blob/b7100575f614470d08f692e1cf7482103e1c413f92da55c0073db0ce2123dfb3
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.