ArticleBMC bioinformatics2020
VFFVA: dynamic load balancing enables large-scale flux variability analysis.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model.PLoS computational biology · 2023Article
- pymgpipe: microbiome metabolic modeling in Python.Journal of open source software · 2023Article
- An improved algorithm for flux variability analysis.BMC bioinformatics · 2022Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- A gap-filling algorithm for prediction of metabolic interactions in microbial communities.PLoS computational biology · 2021Article
- ACHR.cu: GPU-accelerated sampling of metabolic networks.Journal of open source software · 2019Article
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Abstract
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 .
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