scikit-bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

2.86x

Quality

66%

Does it follow best practices?

Impact

63%

2.86x

Average score across 3 eval scenarios

Securityby

Passed

No findings from the security scan

Fix and improve this skill with Tessl

tessl review fix ./skills/bio/scikit-bio/SKILL.md

Quality

Content

65%Weight 40%Scale 1-3

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

The content is highly actionable with executable code across all major capabilities, but it is verbose for a SKILL.md, its multi-step workflows lack validation checkpoints, and it defers to an api_reference.md that does not exist.

Suggestions

Create references/api_reference.md and move the extended method notes, ecosystem integration prose, and per-capability 'Important notes' there so SKILL.md stays a lean overview.

Add explicit validation/checkpoint steps to the Common Workflows (e.g., assert integer counts before diversity, confirm DistanceMatrix symmetry before PERMANOVA) to raise workflow clarity.

Trim conceptual explanations Claude already knows (sequence-type definitions, what ordination 'reduces') to tighten conciseness.

Dimension	Reasoning	Score
Conciseness	The ~430-line body is mostly efficient API cataloguing but pads it with concepts Claude already knows (e.g., defining DNA/RNA/protein, 'reduce high-dimensional data to visualizable spaces') and inline detail that the deferred api_reference.md is meant to hold; it could be tightened rather than left verbose.	2 / 3
Actionability	Numerous executable, real-signature code blocks (skbio.DNA.read, alpha_diversity('shannon', ...), pcoa(dm), permanova(...)) make the guidance copy-paste ready, matching the fully-executable anchor rather than the pseudocode level below.	3 / 3
Workflow Clarity	The 'Common Workflows' section lists four sequences (e.g., Read BIOM table -> diversity -> PCoA -> PERMANOVA) but they lack validation checkpoints or error-recovery feedback loops, matching the 'steps listed but checkpoints missing' anchor.	2 / 3
Progressive Disclosure	The body signals references/api_reference.md, but no references/scripts/assets directories exist, so the pointer is broken and the detailed content stays inline; this matches 'structure present but references not valid / content that should be separate is inline' rather than the clean one-level-deep anchor.	2 / 3
	Total	9 / 12 Passed

Description

67%Weight 40%Scale 1-3

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 is specific and occupies a clear niche, but it omits an explicit 'Use when...' trigger and over-relies on technical metric names, so it answers 'what' well while 'when' is only implied.

Suggestions

Add an explicit trigger clause such as 'Use when working with biological sequences, phylogenetic trees, diversity metrics, or microbiome data' to raise completeness.

Soften technical jargon (PERMANOVA, UniFrac, PCoA) with plain-language keywords a user would naturally say (e.g., 'microbiome stats', 'tree building', 'distance-based statistics').

Lead with a verb-first capability summary (e.g., 'Analyzes biological data...') to keep a consistent third-person action voice.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions including 'Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O', matching the anchor for multiple specific concrete actions rather than the partial domain-only level below.	3 / 3
Completeness	It thoroughly answers 'what' but lacks an explicit 'Use when...' trigger clause, and the rubric caps completeness at 2 when explicit trigger guidance is missing (only an implied 'for microbiome analysis').	2 / 3
Trigger Term Quality	It includes relevant terms like 'microbiome analysis', 'alignments', and 'phylogenetic trees', but leans on technical jargon (PERMANOVA, UniFrac, PCoA) and omits common user-facing variations; not the broad natural-keyword coverage of the top anchor.	2 / 3
Distinctiveness Conflict Risk	The bioinformatics/microbiome niche is sharply defined and unlikely to overlap with other skills, matching the clear-niche anchor; it does not fall to 2 because the domain is distinct rather than merely 'somewhat specific'.	3 / 3
	Total	10 / 12 Passed

Validation

87%

Warnings & errors only

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

Validation — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_version	'metadata.version' is missing	Warning
referenced_paths_exist	Referenced path issues: 1 missing	Warning

	Total	14 / 16 Passed

Repository: wu-yc/LabClaw
Path: skills/bio/scikit-bio/SKILL.md
Commit: df37802

Reviewed: 18 days ago

Table of Contents

Discovery Implementation Validation

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.