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biopython

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.

69

Quality

86%

Does it follow best practices?

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SecuritybySnyk

High

Do not use without reviewing

SKILL.md
Quality
Evals
Security

Quality

Content

72%

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

A well-organized, highly actionable skill body that delegates detail to seven verified reference files and supplies many executable examples. Its main weakness is verbosity from repeated capability enumeration and a time-sensitive version/date stated outside a deprecated section, plus a main workflow lacking explicit validation checkpoints.

Suggestions

Collapse the redundant capability lists — pick one of 'When to Use This Skill' or 'Core Capabilities' and have the other point to it, since both overlap the per-module 'Use for' bullets.

Move the 'Biopython 1.85 (released January 2025)' version/date into an explicitly labeled version/deprecation section so it does not penalize conciseness.

Add an explicit validation checkpoint to the General Workflow Guidelines (e.g. 'run on a small sample and confirm output before scaling to batch/Entrez operations') to lift workflow clarity above 2.

DimensionReasoningScore

Conciseness

Capabilities are enumerated three times — "When to Use This Skill" (12 bullets), "Core Capabilities" (7 items), and each module's "Use for" list — and the time-sensitive "Biopython 1.85 (released January 2025)" version/date is stated inline rather than in a deprecated section, so it is mostly efficient but could be tightened. Not a 3 because tokens are repeated rather than each earning their place; not a 1 because the bulk is actionable technical content rather than concepts Claude already knows.

2 / 3

Actionability

Provides copy-paste-ready executable code for every module plus four complete "Common Patterns" pipelines (GenBank fetch, sequence analysis, BLAST+fetch, tree building), matching the 'fully executable code/commands; specific examples' anchor.

3 / 3

Workflow Clarity

The "General Workflow Guidelines" gives a numbered 4-step sequence (identify module → read reference → extract patterns → combine) but lacks explicit validation checkpoints, and the skill involves batch/destructive operations (Entrez batch download, large-file processing) where the rubric caps workflow clarity at 2 without validation gates. Not a 1 because steps are clearly sequenced and error-handling appears in the code sections.

2 / 3

Progressive Disclosure

The body is an overview with clearly signaled one-level-deep references (e.g. "**Reference:** `references/sequence_io.md`") for each module, all seven referenced files verified to exist, with only quick examples kept inline — matching the 'clear overview with well-signaled one-level-deep references' anchor.

3 / 3

Total

10

/

12

Passed

Description

100%

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

A strong, specific description with explicit use-when triggers and helpful disambiguation against adjacent skills. It names concrete capabilities and natural trigger terms without padding.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — "sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics", "programmatic NCBI/PubMed access", "batch processing, custom bioinformatics pipelines, BLAST automation" — matching the 'lists multiple specific concrete actions' anchor.

3 / 3

Completeness

Explicitly answers 'what' ("Comprehensive molecular biology toolkit") and 'when' via explicit triggers ("Use for...", "Best for..."), so both halves are present and explicit.

3 / 3

Trigger Term Quality

Covers natural user terms a bioinformatician would say — FASTA, GenBank, PDB, NCBI, PubMed, BLAST, bioinformatics pipelines — giving good coverage of common phrasings.

3 / 3

Distinctiveness Conflict Risk

Has a clear molecular-biology niche and explicitly routes to neighboring skills ("For quick lookups use gget; for multi-service integration use bioservices"), making conflict unlikely.

3 / 3

Total

12

/

12

Passed

Validation

87%

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

Validation14 / 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

Total

14

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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