GEMtractor: extracting views into genome-scale metabolic models



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 - a public version is available at


DOI: 10.1093/bioinformatics/btaa068

Projects: BESTER

Publication type: Journal

Journal: Bioinformatics

Editors: Jinbo Xu

Citation: Bioinformatics

Date Published: 31st Jan 2020

Registered Mode: by DOI

Authors: Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi

Scharm, M., Wolkenhauer, O., Jalili, M., & Salehzadeh-Yazdi, A. (2020). GEMtractor: extracting views into genome-scale metabolic models. In J. Xu (Ed.), Bioinformatics (Vol. 36, Issue 10, pp. 3281–3282). Oxford University Press (OUP).

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Created: 1st Apr 2020 at 15:07

Last updated: 1st Apr 2020 at 15:08

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