Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions.

ABSTRACT: Uncertainty in the structure and parameters of networks is ubiquitous across computational biology. In constraint-based reconstruction and analysis of metabolic networks, this uncertainty is present both during the reconstruction of networks and in simulations performed with them. Here, we present Medusa, a Python package for the generation and analysis of ensembles of genome-scale metabolic network reconstructions. Medusa builds on the COBRApy package for constraint-based reconstruction and analysis by compressing a set of models into a compact ensemble object, providing functions for the generation of ensembles using experimental data, and extending constraint-based analyses to ensemble scale. We demonstrate how Medusa can be used to generate ensembles and perform ensemble simulations, a

SUBMITTER: Medlock GL 

PROVIDER: S-EPMC7213742 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature