cobrapy

# 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: ```python from cobra.io import load_model # Load bundled test models model = load_model("textbook") # E. coli core model model = load_model("ecoli") # Full E. coli model model = load_model("salmonella") # Load from files from cobra.io import read_sbml_model, load_json_model, load_yaml_model model = read_sbml_model("path/to/model.xml") model = load_json_model("path/to/model.json") model = load_yaml_model("path/to/model.yml") ``` Save models in various formats: ```python from cobra.io import write_sbml_model, save_json_model, save_yaml_model write_sbml_model(model, "output.xml") # Preferred format save_json_model(model, "output.json") # For Escher compatibility save_yaml_model(model, "output.yml") # Human-readable ``` ### 2. Model Structure and Components Access and inspect model components: ```python # Access components model.reactions # DictList of all reactions model.metabolites # DictList of all metaboli...