Skill audit report
alterlab-biopython Audit report.
Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BLAST, or fetching records from Entrez — for quick one-off database lookups use gget, for unified multi-service integration use bioservices. Part of the AlterLab Academic Skills suite.
OpenAgentSkill Trust Score
OpenAgentSkill Trust Score
The Trust Score helps an agent decide whether a skill is safe enough to shortlist before installation.
GitHub adoption
WARN48
66 GitHub stars
Stars/forks activity
WARN48
66 stars, 13 forks; issue activity unavailable in current metadata
Recent maintenance
PASS88
2mo since push
License clarity
PASS86
MIT
README/SKILL.md completeness
PASS86
Metadata includes enough usage and workflow context
Dependency/runtime risk
FAIL38
command execution surface, credential or environment access
Install availability
PASS92
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-biopython
Install command safety
PASS92
standard package or runtime install path
Permission surface
FAIL18
secrets or environment access, shell or command execution
Repository evidence
PASS86
https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-biopython
Review status
INFO66
AI review data available
Agent Proven outcomes
INFO54
No agent outcome data yet
Checks
Install and adoption review
Install path
92
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-biopython
Repository
88
https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-biopython
License
86
MIT
Maintenance
88
2mo since push
AI review
55
The SKILL.md references Biopython 1.87 as the current version, which may become outdated; consider noting that version numbers change and recommend checking the official docs.
README/SKILL.md completeness
86
Usable description available
Dependency risk
38
command execution surface, credential or environment access
Install command safety
92
standard package or runtime install path
Permission surface
18
secrets or environment access, shell or command execution
Stars/forks activity
48
66 stars, 13 forks; issue activity unavailable in current metadata
Adoption
68
66 GitHub stars
Warnings
- Dependency or permission surface needs review
- Permission surface may require sandboxing
- The SKILL.md references Biopython 1.87 as the current version, which may become outdated; consider noting that version numbers change and recommend checking the official docs.
- The skill's allowed-tools include broad Bash(python:*) and Bash(uv:*), which is typical for coding skills but could be misused if the agent is compromised; however, this is a configuration concern, not a flaw in the skill itself.
- Quality score needs review
- Permission surface needs review: secrets or environment access, shell or command execution
- GitHub adoption: 66 GitHub stars
- Stars/forks activity: 66 stars, 13 forks; issue activity unavailable in current metadata
- Dependency/runtime risk: command execution surface, credential or environment access
- Permission surface: secrets or environment access, shell or command execution
Method
This report combines public metadata, AI review output, repository freshness, install readiness, OpenAgentSkill events, quality scoring, trust checks, and the agent safety gate. It is not a full source-code security review.
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