bioinformatics

Gateway to 400+ genomics and computational biology skills.

Quality

65%

Does it follow best practices?

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Securityby

Low

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tessl review fix ./optional-skills/research/bioinformatics/SKILL.md

Quality

Content

82%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.

A well-executed gateway skill: concrete clone/read commands, a comprehensive domain-organized index, and useful non-obvious pitfalls (format mismatch, prerequisites, disk space). Minor improvements possible in deduplicating the format warning and making prerequisite checks an explicit workflow step.

Dimension	Reasoning	Score
Conciseness	The body is a lean catalog with no explanations of concepts Claude already knows; the environment setup and pitfalls sections are dense and non-obvious. Minor redundancy keeps it from 5: step 4's 'These are NOT Hermes-format skills — treat them as expert domain guides' is restated nearly verbatim in the Pitfalls section.	4 / 5
Actionability	Fully executable, copy-paste-ready commands throughout: shallow `git clone` commands for both repos, exact `cat` paths showing each repo's directory layout, per-platform install commands (apt, brew, conda, pip, BiocManager), and the ClawBio prerequisite (`pip install -r requirements.txt`). The common cases (find a skill, fetch it, read it) are covered with specific examples.	5 / 5
Workflow Clarity	The 4-step fetch workflow (identify from index → shallow clone → read the specific skill → follow as reference) is clearly numbered with concrete commands at each step. It is not 5 because validation checkpoints are implicit rather than in the sequence — prerequisite checking appears only as a Pitfalls note ('Check prerequisites before running pipelines'), not as an explicit step or feedback loop.	4 / 5
Progressive Disclosure	No bundle files exist, and the ~150-line skill index is inlined in SKILL.md — but for a gateway skill that index is the routing mechanism, so inline placement is functionally justified, and it is cleanly sectioned by domain with consistent bioSkills/ClawBio labeling. It is not 5 because the index could arguably live in a references/ file to keep the entry point leaner, leaving a compact routing summary in SKILL.md.	4 / 5
	Total	17 / 20 Passed

Description

48%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 is brief and names a distinct domain, but it functions as a title rather than a trigger: it contains no concrete actions, no 'Use when...' guidance, and misses the most natural keyword ('bioinformatics'). The body's excellent trigger clause should be reflected in the description itself.

Suggestions

Add an explicit 'Use when...' clause to the description, e.g. 'Use when asked about bioinformatics, genomics, sequencing, variant calling, gene expression, or any computational biology task.'

Include the most natural user term 'bioinformatics' and other common trigger words (sequencing, DNA, RNA-seq, single-cell) in the description field itself, not just the body.

State the concrete action the skill performs, e.g. 'Indexes 400+ genomics and computational biology skills and fetches the right one on demand' instead of the structural label 'Gateway to'.

Dimension	Reasoning	Score
Specificity	The description names the domain ('genomics and computational biology') and the scale ('400+ skills') but describes no concrete actions — 'Gateway' is a structural role, not an actionable capability like 'indexes' or 'fetches'. This matches the anchor 'Names the domain but actions are minimal or generic'; it falls short of 3 because no concrete actions are listed at all.	2 / 5
Completeness	The 'what' is reasonably clear (a gateway to 400+ skills) but the 'when' is entirely absent — the strong 'Use when asked about bioinformatics...' clause exists only in the body, not the description. Per the guidelines, a missing 'Use when...' clause caps completeness at 3; it is not 2 because the 'what' is not vague.	3 / 5
Trigger Term Quality	'genomics' and 'computational biology' are relevant keywords, but the description omits the most natural user term ('bioinformatics' — the skill's own name) plus common variations like 'sequencing', 'variant calling', 'DNA', or 'RNA-seq'. Some relevant keywords with missing synonyms matches anchor 3; coverage is not good enough for 4.	3 / 5
Distinctiveness Conflict Risk	'genomics and computational biology skills' carves a clear niche with minimal conflict risk against non-biological skills. It is not 5 because the 400+ skill breadth spans nearly every biology subdomain, creating minor overlap risk with dedicated single-purpose skills (e.g., a standalone variant-calling or DESeq2 skill).	4 / 5
	Total	12 / 20 Passed

Validation

81%

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 — 13 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_version	'metadata.version' is missing	Warning
metadata_field	'metadata' should map string keys to string values	Warning
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	13 / 16 Passed

Repository: NousResearch/hermes-agent
Path: optional-skills/research/bioinformatics/SKILL.md
Commit: 68fa7e9

Reviewed: 3 days ago

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