EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search

• Published in: BMC bioinformatics Vol. 22; no. 1; pp. 1 - 21
• Main Authors: Buchner, Bianca A, Zanghellini, Jürgen
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 10.11.2021; Springer Nature B.V; BioMed Central; BMC
• Subjects: Algorithms; Biotechnology; Cobrapy; Computation; Constraint satisfaction; Elementary modes; Enumeration; Genomes; Lexicographic reverse search; Linear programming; Metabolic engineering; Metabolic modelling; Metabolic networks; Metabolism; Methods; Mplrs; Source programs; Systems biology; Variables; Workflow; Austria
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04417-9

Elementary flux mode (EFM) analysis is a well-established, yet computationally challenging approach to characterize metabolic networks. Standard algorithms require huge amounts of memory and lack scalability which limits their application to single servers and consequently limits a comprehensive analysis to medium-scale networks. Recently, Avis et al. developed mplrs--a parallel version of the lexicographic reverse search (lrs) algorithm, which, in principle, enables an EFM analysis on high-performance computing environments (Avis and Jordan. mplrs: a scalable parallel vertex/facet enumeration code. arXiv:1511.06487, 2017). Here we test its applicability for EFM enumeration. We developed EFMlrs, a Python package that gives users access to the enumeration capabilities of mplrs. EFMlrs uses COBRApy to process metabolic models from sbml files, performs loss-free compressions of the stoichiometric matrix, and generates suitable inputs for mplrs as well as efmtool, providing support not only for our proposed new method for EFM enumeration but also for already established tools. By leveraging COBRApy, EFMlrs also allows the application of additional reaction boundaries and seamlessly integrates into existing workflows. We show that due to mplrs's properties, the algorithm is perfectly suited for high-performance computing (HPC) and thus offers new possibilities for the unbiased analysis of substantially larger metabolic models via EFM analyses. EFMlrs is an open-source program that comes together with a designated workflow and can be easily installed via pip.