PLoS Computational Biology
Public Library of Science
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Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions
Volume: 16, Issue: 4
DOI 10.1371/journal.pcbi.1007847
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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, and how machine learning can be used in conjunction with Medusa to guide the curation of genome-scale metabolic network reconstructions. Medusa is available under the permissive MIT license from the Python Packaging Index (https://pypi.org) and from github (https://github.com/opencobra/Medusa), and comprehensive documentation is available at https://medusa.readthedocs.io/en/latest.

https://www.researchpad.co/tools/openurl?pubtype=article&doi=10.1371/journal.pcbi.1007847&title=Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions&author=Gregory L. Medlock,Thomas J. Moutinho,Jason A. Papin,Hugues Berry,Douglas A Lauffenburger,Hugues Berry,Douglas A Lauffenburger,Hugues Berry,Douglas A Lauffenburger,Hugues Berry,Douglas A Lauffenburger,Hugues Berry,&keyword=&subject=Research Article,Research and Analysis Methods,Simulation and Modeling,Biology and Life Sciences,Biochemistry,Metabolism,Metabolites,Computer and Information Sciences,Network Analysis,Metabolic Networks,Computer and Information Sciences,Artificial Intelligence,Machine Learning,Biology and Life Sciences,Molecular Biology,Molecular Biology Techniques,Molecular Biology Assays and Analysis Techniques,Combined Bisulfite Restriction Analysis,Research and Analysis Methods,Molecular Biology Techniques,Molecular Biology Assays and Analysis Techniques,Combined Bisulfite Restriction Analysis,Biology and Life Sciences,Genetics,Genomics,Biology and Life Sciences,Organisms,Bacteria,Staphylococcus,Staphylococcus Aureus,Biology and Life Sciences,Microbiology,Medical Microbiology,Microbial Pathogens,Bacterial Pathogens,Staphylococcus,Staphylococcus Aureus,Medicine and Health Sciences,Pathology and Laboratory Medicine,Pathogens,Microbial Pathogens,Bacterial Pathogens,Staphylococcus,Staphylococcus Aureus,Biology and Life Sciences,Biophysics,Biophysical Simulations,Physical Sciences,Physics,Biophysics,Biophysical Simulations,Biology and Life Sciences,Computational Biology,Biophysical Simulations,