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bioRxiv · 10.1101/790725

GEMtractor: Extracting Views into Genome-scale Metabolic Models

Scharm, M.·Wolkenhauer, O.·Jalili, M.·Salehzadeh-Yazdi, A.
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Abstract

SummaryComputational metabolic models typically encode for graphs of species, reactions, and enzymes. Comparing genome-scale models through topological analysis of multipartite graphs is challenging. However, in many practical cases it is not necessary to compare the full networks. The GEMtractor is a web-based tool to trim models encoded in SBML. It can be used to extract subnetworks, for example focusing on reaction- and enzyme-centric views into the model.\n\nAvailability and ImplementationThe GEMtractor is licensed under the terms of GPLv3 and developed at github.com/binfalse/GEMtractor - a public version is available at sbi.uni-rostock.de/gemtractor.\n\nContactmartin.scharm@uni-rostock.de and ali.salehzadeh-yazdi@uni-rostock.de

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Scharm, M., Wolkenhauer, O., Jalili, M., Salehzadeh-Yazdi, A.. 2019-10-02. GEMtractor: Extracting Views into Genome-scale Metabolic Models. https://doi.org/10.1101/790725

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