Ecmtool: fast and memory-efficient enumeration of elementary conversion modes.

ABSTRACT:

Motivation

Characterizing all steady-state flux distributions in metabolic models remains limited to small models due to the explosion of possibilities. Often it is sufficient to look only at all possible overall conversions a cell can catalyze ignoring the details of intracellular metabolism. Such a characterization is achieved by elementary conversion modes (ECMs), which can be conveniently computed with ecmtool. However, currently, ecmtool is memory intensive, and it cannot be aided appreciably by parallelization.

Results

We integrate mplrs-a scalable parallel vertex enumeration method-into ecmtool. This speeds up computation, drastically reduces memory requirements and enables ecmtool's use in standard and high-performance computing environments. We show the new capabili

SUBMITTER: Buchner B 

PROVIDER: S-EPMC9982354 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature