MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.

ABSTRACT: Mathematical models of metabolic networks utilize simulation to study system-level mechanisms and functions. Various approaches have been used to model the steady state behavior of metabolic networks using genome-scale reconstructions, but formulating dynamic models from such reconstructions continues to be a key challenge. Here, we present the Mass Action Stoichiometric Simulation Python (MASSpy) package, an open-source computational framework for dynamic modeling of metabolism. MASSpy utilizes mass action kinetics and detailed chemical mechanisms to build dynamic models of complex biological processes. MASSpy adds dynamic modeling tools to the COnstraint-Based Reconstruction and Analysis Python (COBRApy) package to provide an unified framework for constraint-based and kinetic modeling of

SUBMITTER: Haiman ZB 

PROVIDER: S-EPMC7872247 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature