VFFVA: dynamic load balancing enables large-scale flux variability analysis

BMC Bioinformatics

Marouen Ben Guebila¹ 

[1] Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA;

关键词: Metabolic models;    Flux variability analysis;    High performance computing;    Systems biology;   

DOI  :  10.1186/s12859-020-03711-2

来源: Springer

【 摘 要 】

BackgroundGenome-scale metabolic models are increasingly employed to predict the phenotype of various biological systems pertaining to healthcare and bioengineering. To characterize the full metabolic spectrum of such systems, Fast Flux Variability Analysis (FFVA) is commonly used in parallel with static load balancing. This approach assigns to each core an equal number of biochemical reactions without consideration of their solution complexity.ResultsHere, we present Very Fast Flux Variability Analysis (VFFVA) as a parallel implementation that dynamically balances the computation load between the cores in runtime which guarantees equal convergence time between them. VFFVA allowed to gain a threefold speedup factor with coupled models and up to 100 with ill-conditioned models along with a 14-fold decrease in memory usage.ConclusionsVFFVA exploits the parallel capabilities of modern machines to enable biological insights through optimizing systems biology modeling. VFFVA is available in C, MATLAB, and Python at https://github.com/marouenbg/VFFVA.

【 授权许可】

CC BY