Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.
Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7602, South Africa.
Bioinformatics. 2020 May 1;36(10):3281-3282. doi: 10.1093/bioinformatics/btaa068.
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.
计算代谢模型通常对物种、反应和酶的图进行编码。通过多部分图的拓扑分析来比较基因组规模的模型具有挑战性。然而，在许多实际情况下，没有必要比较完整的网络。GEMtractor 是一个基于网络的工具，用于修剪以 SBML 编码的模型。它可用于提取子网，例如，专注于模型中以反应和酶为中心的视图。
GEMtractor 根据 GPLv3 许可，并在 github.com/binfalse/GEMtractor 上开发。一个公共版本可在 sbi.uni-rostock.de/gemtractor 上获得。
