Agent skill · research science · davila7
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 domain-specific commands 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 2026-08-06. 30,138 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 davila7/cobrapy