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gsmm-builder

Build or load a genome-scale metabolic model (GSMM) using COBRApy. Covers loading from BIGG, constructing minimal models from scratch, setting medium constraints, and exporting validated .json model files.

61

Quality

72%

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tessl review fix ./external/agents/Biology-Agent/skills/gsmm-builder/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

78%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 executable code and a sensible workflow, but it underuses its bundle reference and omits an explicit validation checkpoint in the main flow. Linking the COBRApy reference and adding a pre-export validation step would raise both weak dimensions.

Suggestions

Add an explicit validation checkpoint in the workflow before export, e.g. 'Run model.optimize() and confirm solution.status == "optimal" before saving' with a fix-retry loop.

Signal the existing reference from the body, e.g. a line like 'Full COBRApy API: See [references/cobra_reference.md](references/cobra_reference.md)', so the bundle is discoverable rather than orphaned.

Trim the Overview's explanation of what a GSMM/stoichiometric matrix is, since Claude already knows this; keep only the skill-specific framing.

DimensionReasoningScore

Conciseness

Mostly efficient with executable code and a tight conventions table, though the Overview paragraph explaining what a GSMM/stoichiometric matrix is could be trimmed as Claude already knows this.

4 / 5

Actionability

Provides copy-paste-ready, executable COBRApy code for loading, building, setting objectives/medium, and exporting, covering the common cases with specific IDs and bounds.

5 / 5

Workflow Clarity

A clear four-step sequence with a failure-modes section, but the main flow lacks an explicit validate→fix→retry checkpoint (e.g. run model.optimize() and check status before export).

4 / 5

Progressive Disclosure

Sections are well organized, but a bundle file (references/cobra_reference.md) exists yet is never referenced or signaled from the body, and API-detail content stays inline.

3 / 5

Total

16

/

20

Passed

Description

66%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 specific and actionable with concrete capabilities and clear niche scoping, but it lacks an explicit 'when to use' trigger clause. Adding a 'Use when...' sentence would lift completeness and trigger guidance.

Suggestions

Add an explicit 'Use when ...' clause naming natural user phrases (e.g. 'Use when building or loading a genome-scale metabolic model, running FBA, or when the user mentions GSMMs, COBRApy, BIGG, or medium constraints').

Include common synonyms/extensions users might say, such as 'FBA', 'flux balance analysis', 'stoichiometric model', or '.xml/.json model files', to broaden trigger-term coverage.

Mirror file extensions already covered in the body (e.g. '.xml SBML models') so the description matches the actual load/export surface.

DimensionReasoningScore

Specificity

Lists several concrete actions — 'loading from BIGG', 'constructing minimal models from scratch', 'setting medium constraints', 'exporting validated .json model files' — with only minor coverage gaps.

4 / 5

Completeness

Has a clear 'what' but no 'Use when...' or equivalent explicit trigger guidance, which caps completeness at 3 per the rubric guidelines.

3 / 5

Trigger Term Quality

Includes natural domain terms like 'genome-scale metabolic model (GSMM)', 'COBRApy', and 'BIGG', but misses a few common variations/synonyms a user might say.

4 / 5

Distinctiveness Conflict Risk

The GSMM/COBRApy/BIGG niche is clearly distinct from other skills with only minor overlap risk with closely related metabolic analysis skills.

4 / 5

Total

15

/

20

Passed

Validation

93%

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

Validation15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

Total

15

/

16

Passed

Repository
aiming-lab/AutoResearchClaw
Reviewed

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