Abstract
Computational 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. The 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.
Highlights
At the most basic abstraction level, biological phenomena can be represented as mathematical graphs
Genome-scale metabolic models (GEMs) are an example, that describe the associations between genes, proteins, and reactions of an organism
Here we introduce the GEMtractor, a web-based tool to extract reaction-centric and enzyme-centric views of genome-scale metabolic models (GEM)
Summary
5 1Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany 6 2Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, 7 Stellenbosch, South Africa 8 3Hematology, Oncology and SCT Research Center, Tehran University of Medical Sciences, Tehran, Iran
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