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biopython

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.

59

Quality

70%

Does it follow best practices?

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Adds up to 20 points to the overall score

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SecuritybySnyk

Passed

No findings from the security scan

Fix and improve this skill with Tessl

tessl review fix ./plugins/AI-Agents-Safe-Coding-Skills/skills/biopython/SKILL.md

The canonical home for this skill is biopython in administrakt0r/AI-Agents-Safe-Coding-Skills

SKILL.md
Quality
Evals
Security

Quality

Content

65%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is highly actionable with comprehensive executable examples, but it is verbose with redundant module listings and a duplicated grep section, lacks validation feedback loops for its batch/database operations, and signals reference files that are not actually present in the bundle.

Suggestions

Remove the redundant Quick Reference grep section (it duplicates General Workflow Guidelines) and the verbatim restatement of the description in the Overview.

List the seven modules once and link to their reference files instead of repeating them in Core Capabilities, Using This Skill, and Summary.

Add explicit validation checkpoints for batch operations — e.g., verify Entrez result counts and retry on HTTP errors before proceeding with downstream parsing.

Either ship the referenced files under references/ or inline their content; dangling references/sequence_io.md etc. break navigation.

DimensionReasoningScore

Conciseness

The body is mostly useful reference material with executable examples, but it repeats content: the frontmatter description is restated verbatim in the Overview, the seven modules are listed three times (Core Capabilities, Using This Skill, Summary), and a grep-pattern "Quick Reference" section duplicates the one in General Workflow Guidelines.

3 / 5

Actionability

It provides abundant copy-paste-ready, executable Python (SeqIO.parse, Entrez.esearch, PDBParser, Phylo tree building) plus concrete install/setup commands covering the common cases across every major module.

5 / 5

Workflow Clarity

A lookup workflow (identify module → read reference → adapt pattern) is present and Common Patterns show pipelines, but batch/destructive operations like Entrez batch downloads and BLAST lack explicit validate→fix→retry checkpoints, which caps workflow clarity at 3.

3 / 5

Progressive Disclosure

References are clearly signaled one level deep (e.g. "Reference: references/sequence_io.md"), but the references/ directory does not exist in the bundle, so all seven referenced paths are dangling, and substantial material (Common Patterns, Best Practices, Troubleshooting) is inlined in SKILL.md rather than split out.

3 / 5

Total

14

/

20

Passed

Description

75%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description clearly communicates what Biopython does with comprehensive, specific capability coverage and strong distinctiveness, but it omits any explicit "when to use" trigger guidance and is missing common file-format/task keywords (FASTA, BLAST, PDB) that users would naturally say.

Suggestions

Add an explicit "Use when ..." clause naming concrete triggers (e.g., parsing FASTA/GenBank/PDB files, running BLAST, building phylogenetic trees).

Include common file extensions and tool names users say (FASTA, FASTQ, GenBank, PDB, BLAST) to improve trigger-term quality.

Drop the catch-all "and many other bioinformatics tasks" to keep the description crisp and avoid over-claiming.

DimensionReasoningScore

Specificity

It lists multiple concrete capability areas — "sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics" — giving comprehensive coverage rather than vague language.

5 / 5

Completeness

The "what" is clear ("comprehensive set of freely available Python tools for biological computation" plus enumerated capabilities), but there is no "Use when..." clause or equivalent explicit trigger guidance, which caps completeness at 3 per the rubric.

3 / 5

Trigger Term Quality

Strong natural terms like "Biopython", "sequence manipulation", and "bioinformatics" are present, but common task-level triggers users actually say (FASTA, GenBank, BLAST, PDB) are missing from the description.

4 / 5

Distinctiveness Conflict Risk

Naming a specific, well-known library ("Biopython") with a distinct bioinformatics niche gives it a clear trigger with minimal overlap risk against other skills.

5 / 5

Total

17

/

20

Passed

Validation

81%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation13 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

referenced_paths_exist

Referenced path issues: 11 missing

Warning

Total

13

/

16

Passed

Repository
administrakt0r/AI-Agents-Safe-Coding-Skills
Reviewed

Table of Contents

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