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

ABSTRACT:

Background

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.

Results

We developed EFMlrs, a Python package that gives users access to the enumeration c

SUBMITTER: Buchner BA 

PROVIDER: S-EPMC8579665 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature