cobrapy

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

1.30x

Quality

73%

Does it follow best practices?

Impact

85%

1.30x

Average score across 6 eval scenarios

Securityby

Passed

No known issues

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/cobrapy/SKILL.md

Evaluation results

73%

18%

Metabolic Flux Flexibility Study in E. coli

FVA and flux sampling analysis

Criteria

Without context

With context

Loopless FVA used

fraction_of_optimum set

100%

OptGP sampling method

100%

Parallel sampling processes

Sample validation performed

50%

100%

Validation result reported

75%

100%

slim_optimize for baseline

100%

FVA results exported

100%

Flux samples exported

100%

Solution status checked

FVA at both levels

100%

94%

30%

Minimal Growth Media Identification for E. coli Fermentation

Minimal media design and medium manipulation

Criteria

Without context

With context

minimize_components=True

100%

Medium reassigned as dict

100%

Context manager for temp changes

100%

slim_optimize used

100%

Anaerobic condition set

62%

50%

Aerobic medium CSV

100%

Anaerobic medium CSV

100%

Media comparison report

100%

Solution status checked

100%

model.medium used for medium access

80%

90%

12%

Metabolic Pathway Analysis for Acetate Production Strain

Parsimonious FBA and production strain analysis

Criteria

Without context

With context

pfba used

100%

Context manager for objective change

100%

slim_optimize for baseline

100%

Solution status checked

50%

100%

Bounds set with .bounds

SBML format for saving

100%

Solution comparison CSV

100%

Growth coupling scan CSV

100%

Total flux comparison reported

100%

Growth constraint applied

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: b58ad7e

Evaluated: 25 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Metabolic Flux Flexibility Study in E. coli Minimal Growth Media Identification for E. coli Fermentation Metabolic Pathway Analysis for Acetate Production Strain

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