Agent skill · research science · aiskillstore
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Why this skill is useful
Provides specific commands and functions for metabolic modeling that the AI wouldn't reliably generate on its own.
What it needs
Requires cobra installed locally. About 6k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
COBRApy - Constraint-Based Reconstruction and Analysis Overview COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, essential for systems biology research. Work with genome-scale metabolic models, perform computational simulations of cellular metabolism, conduct metabolic engineering analyses, and predict phenotypic behaviors. Core Capabilities COBRApy provides comprehensive tools organized into several key areas: 1. Model Management Load existing models from repositories or files: Save models in various formats: 2. Model Structure and Components Access and inspect model components: 3. Flux Balance Analysis (FBA) Perform standard FBA simulation: Parsimonious FBA (minimize total flux): Geometric FBA (find central solution): 4. Flux Variability Analysis (FVA) Determine flux ranges for all reactions: 5. Gene and Reaction Deletion Studies Perform knockout analyses: 6. Growth Media and Minimal Media Manage growth medium: 7. Flux Sampling Sample the feasible flux space: 8. Production Envelopes Calculate phenotype phase planes: 9. Gapfilling Add reactions to make models feasible: 10. Model Building Build models from scratch: Common Workflows Workflow 1: Load Model and Predict Growth Workflow 2: Gene Knockout Screen Workflow 3: Media Optimization Workflow 4: Flux Uncertainty Analysis Workflow 5: Context Manager for Temporary Changes Use context managers to make temporary modifications: Key Concepts DictList Objects Models use DictList objects for reactions, metabolites, and genes - behaving like both lists and dictionaries: Flux Constraints Reaction bounds define feasible flux ranges: Irreversible: lowerbound = 0, upperbound > 0 Reversible: lowerbound < 0, upperbound > 0 Set both bounds simultaneously with .bounds to avoid inconsistencies Gene-Reaction Rules (GPR) Boolean logic linking genes to reactions: Exchange Reactions Special reactions representing metabolite import/export: Named with prefix EX by convention Positi …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/cobrapy--21bbb5