GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization

Bioinformatics
Yu-Chieh LiaoChao A Hsiung

Abstract

Genome-scale metabolic network models have become an indispensable part of the increasingly important field of systems biology. Metabolic systems biology studies usually include three major components-network model construction, objective- and experiment-guided model editing and visualization, and simulation studies based mainly on flux balance analyses. Bioinformatics tools are required to facilitate these complicated analyses. Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components is not yet available. Here we present a software platform, GEMSiRV (GEnome-scale Metabolic model Simulation, Reconstruction and Visualization), to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies. GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-gen...Continue Reading

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Citations

Jun 15, 2013·Bioinformatics·John W MayChristoph Steinbeck
Oct 14, 2014·BioMed Research International·Joseph KoussaKourosh Salehi-Ashtiani
Oct 27, 2015·Frontiers in Microbiology·Neema Jamshidi, Anu Raghunathan
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Apr 16, 2016·PLoS Computational Biology·Brian R GrangerZhenjun Hu
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Aug 9, 2019·Genome Biology·Sebastián N MendozaBas Teusink
Dec 15, 2020·Metabolic Engineering·Irene Otero-Muras, Pablo Carbonell

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