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cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

61

Quality

73%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

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tessl review fix ./backend/cli/skills/biology/cobrapy/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

65%

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 throughout, but it is over-long and duplicates content already in the bundled references, weakening conciseness and progressive disclosure. Workflow validation checkpoints are present only implicitly.

Suggestions

Trim the inline capability sections into a concise overview and defer exhaustive examples to references/workflows.md and references/api_quick_reference.md, linking each section explicitly.

Add explicit validate→fix→retry feedback loops for batch/risky operations (e.g. check solution.status after optimize, re-validate sampled fluxes before reporting).

Replace prose that restates API behavior with one-line pointers to the API quick reference to reduce token load.

DimensionReasoningScore

Conciseness

The ~450-line body is mostly executable code with little concept padding, but it substantially overlaps the bundled references and could be tightened by pushing per-capability detail into those files.

2 / 3

Actionability

Every section provides complete, copy-paste-ready Python (e.g. load_model, model.optimize(), single_gene_deletion) with real imports and arguments, matching the fully-executable anchor.

3 / 3

Workflow Clarity

Workflows 1–5 are sequenced and best practices mention checking status/validating, but there are no explicit validate→fix→retry feedback loops for batch operations like double deletions or sampling, so it sits at 2.

2 / 3

Progressive Disclosure

The two referenced files (references/workflows.md, references/api_quick_reference.md) are real and one level deep, but the main SKILL.md is a monolithic wall of inline capability detail that largely duplicates those references rather than being a lean overview pointing to them.

2 / 3

Total

9

/

12

Passed

Description

82%

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 trigger-rich with a clear niche, but it lacks an explicit 'Use when…' clause so the 'when to use it' guidance is only implied. Adding a direct trigger sentence would raise completeness.

Suggestions

Append an explicit trigger clause, e.g. 'Use when working with genome-scale metabolic models, running FBA/FVA, or performing gene knockout studies.'

Consider adding a few user-natural phrasings like 'metabolic model' or 'growth medium' to broaden trigger coverage.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'FBA, FVA, gene knockouts, flux sampling, SBML models' — matching the top anchor of naming several specific capabilities rather than vague language.

3 / 3

Completeness

Clearly states what the skill does, but the 'when' is only implied via 'for systems biology and metabolic engineering analysis' rather than an explicit 'Use when…' trigger clause, so it is capped at 2 per the guidelines.

2 / 3

Trigger Term Quality

Includes natural terms a systems-biology user would actually say ('FBA', 'FVA', 'gene knockouts', 'flux sampling', 'metabolic modeling', 'COBRA'), giving good coverage of common phrasings.

3 / 3

Distinctiveness Conflict Risk

The constraint-based metabolic modeling / COBRA niche is specific with distinct domain triggers, making it unlikely to fire for unrelated skills.

3 / 3

Total

11

/

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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