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

Martin Scharm^*
, Olaf Wolkenhauer
, Mahdi Jalili
, Ali Salehzadeh-Yazdi

^*Corresponding author for this work

University of Rostock
Stellenbosch University
Hematology, Oncology and Stem Cell Transplantation Research Center

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

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.

Original language	English
Pages (from-to)	3281-3282
Number of pages	2
Journal	Bioinformatics
Volume	36
Issue number	10
DOIs	https://doi.org/10.1093/bioinformatics/btaa068
State	Published - 1 May 2020
Externally published	Yes

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10.1093/bioinformatics/btaa068

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title = "GEMtractor: Extracting views into genome-scale metabolic models",

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.",

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AU - Wolkenhauer, Olaf

AU - Jalili, Mahdi

AU - Salehzadeh-Yazdi, Ali

PY - 2020/5/1

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N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85084692958

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M3 - Article

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GEMtractor: Extracting views into genome-scale metabolic models

Abstract

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