GEMtractor: extracting views into genome-scale metabolic models

Martin Scharm; Olaf Wolkenhauer; Mahdi Jalili; Ali Salehzadeh-Yazdi

doi:10.1093/bioinformatics/btaa068

GEMtractor: extracting views into genome-scale metabolic models

Bioinformatics. 2020 May 1;36(10):3281-3282. doi: 10.1093/bioinformatics/btaa068.

Authors

Martin Scharm¹, Olaf Wolkenhauer^{1

2}, Mahdi Jalili³, Ali Salehzadeh-Yazdi¹

Affiliations

¹ Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.
² Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7602, South Africa.
³ Hematology, Oncology and SCT Research Center, Tehran University of Medical Sciences, Tehran, 1416753955 Iran.

PMID: 32003785
DOI: 10.1093/bioinformatics/btaa068

Abstract

Summary: 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.

Availability and implementation: 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome*
Metabolic Networks and Pathways* / genetics
Models, Biological
Software