bioinformatics

Gateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more. Fetches domain-specific reference material on demand.

Quality

68%

Does it follow best practices?

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Securityby

Medium

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Fix and improve this skill with Tessl

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

Quality

Content

65%

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 gateway with concrete clone/read/install commands, but the full skill index is inlined rather than progressively disclosed and the fetch workflow lacks explicit validation checkpoints.

Suggestions

Move the complete skill index into a separate reference file (e.g., SKILL_INDEX.md) and keep a compact domain overview in SKILL.md, linking to it for both conciseness and progressive disclosure.

Add validation checkpoints to the fetch workflow — e.g., after cloning, verify the repo directory and the specific skill path exist before reading it; confirm prerequisites are installed before running ClawBio pipelines.

Add an explicit error-recovery note for when a named skill is not found in the index or a clone fails, giving the workflow a feedback loop.

Dimension	Reasoning	Score
Conciseness	The body avoids concept-explanation fluff and uses concrete commands, but it inlines the entire 400+ skill index (~150 lines) where a compact overview plus a separate index would be leaner, so it is 'mostly efficient but could be tightened'.	2 / 3
Actionability	Real executable commands throughout — shallow `git clone`, specific `cat` paths into the cloned repos, and complete pip/R/apt/brew/conda install blocks — make the guidance copy-paste ready.	3 / 3
Workflow Clarity	The 'How to fetch and use a skill' section is a clear numbered 4-step sequence, but it lacks explicit validation checkpoints (e.g., confirm the clone succeeded, verify the skill path exists), so checkpoints are implicit.	2 / 3
Progressive Disclosure	No bundle files exist and external repo references are well signaled with URLs and paths, but the full skill index is inlined in SKILL.md rather than split into a one-level-deep reference file, matching the 'content that should be separate is inline' anchor.	2 / 3
	Total	9 / 12 Passed

Description

72%

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 well-targeted, distinctive gateway description with strong natural trigger terms, but it lacks an explicit 'Use when…' clause and describes only a single concrete action, capping completeness and specificity.

Suggestions

Add an explicit 'Use when…' clause (e.g., 'Use when the user asks about genomics, variant calling, single-cell analysis, or any computational biology task') so completeness can reach 3.

Spell out more concrete actions beyond 'fetches' — e.g., 'Indexes 400+ skills, fetches the matching reference or pipeline, and applies it to the task' — to lift specificity.

Lead with the core action before enumerating domains so the capability is clear in the first sentence.

Dimension	Reasoning	Score
Specificity	Names the bioinformatics domain exhaustively but offers only one concrete action ("Fetches domain-specific reference material on demand") rather than a list of distinct actions, matching the 'names domain and some actions, but not comprehensive' anchor.	2 / 3
Completeness	It clearly states what the skill does (gateway/index that fetches reference material) but has no explicit 'Use when…' trigger clause, so the 'when' is only implied — per the guideline this caps completeness at 2.	2 / 3
Trigger Term Quality	"genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology" are exactly the natural terms a bioinformatics user would say, giving good coverage.	3 / 3
Distinctiveness Conflict Risk	A clearly delineated bioinformatics niche with domain-specific trigger terms makes it unlikely to fire for unrelated skills.	3 / 3
	Total	10 / 12 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: 4c9628e

Reviewed: about 14 hours ago

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