COBRApy

COBRApy is a Python package for metabolic modeling. It provides tools for constructing, simulating, and analyzing metabolic networks. Metabolic models are mathematical representations of biochemical reaction networks within cells. COBRApy allows researchers to study cellular metabolism, predict the effects of genetic or environmental changes, and design metabolic engineering strategies.

The core functionality of COBRApy includes reading and writing metabolic models in various standard formats, such as SBML and JSON. It enables the simulation of these models using flux balance analysis (FBA), a method that determines the flux distribution through the metabolic network under steady-state conditions. This allows for the prediction of growth rates, substrate consumption, and product formation.

COBRApy also offers advanced analysis capabilities. These include identifying essential genes or reactions, performing sensitivity analysis to understand the impact of parameter changes, and optimizing metabolic pathways for specific objectives. The package is designed to be user-friendly and integrates well with other scientific Python libraries like NumPy and SciPy, facilitating complex computational biology workflows. Its open-source nature promotes collaboration and development within the systems biology community.