Journal
BIOSYSTEMS
Volume 113, Issue 1, Pages 37-39Publisher
ELSEVIER SCI LTD
DOI: 10.1016/j.biosystems.2013.04.002
Keywords
Elementary mode analysis; Metabolic network analysis; Transcriptional regulatory network; Gene regulation
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Funding
- Austrian BMWFJ
- BMVIT
- SFG
- Standortagentur Tirol
- ZIT through the Austrian FFG-COMET-Funding Program
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Despite the considerable progress made in recent years, the computation of the complete set of elementary flux modes of large or even genome-scale metabolic networks is still impossible. We present regEfmtool which is an extension to efmtool that utilizes transcriptional regulatory networks for the computation of elementary flux modes. The implemented extension significantly decreases the computational costs for the calculation of elementary flux modes, such as runtime, memory usage and disk space by omitting biologically infeasible solutions. Hence, using the presented regEfmtool pushes the size of metabolic networks that can be studied by elementary flux modes to new limits. (c) 2013 Elsevier Ireland Ltd. All rights reserved.
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