cobrapy

Topics in the source

• COBRApy - Constraint-Based Reconstruction and Analysis
• Overview
• Core Capabilities
• 1. Model Management
• 2. Model Structure and Components
• 3. Flux Balance Analysis (FBA)
• 4. Flux Variability Analysis (FVA)
• 5. Gene and Reaction Deletion Studies

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. COBRApy provides comprehensive tools organized into several key areas: Load existing models from repositories or files: Save models in various formats: Access and inspect model components: Perform standard FBA simulation: Parsimonious FBA (minimize total flux): Geometric FBA (find central solution): Determine flux ranges for all reactions: Perform knockout analyses: Manage growth medium: Sample the feasible flux space: Calculate phenotype phase planes: Add reactions to make models feasible: Build models from scratch: Use context managers to make temporary modifications: Models use DictList objects for reactions, metabolites, and genes - behaving like both lists and dictionaries: Reaction bounds define feasible flux ranges: Irreversible: lowerbound = 0, upperbound > 0 Reversible: lowerbound 0 Set both bounds simultaneously with .bounds to avoid inconsistencies Boolean l

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