LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models.

ABSTRACT:

Background

Uniform random sampling of mass-balanced flux solutions offers an unbiased appraisal of the capabilities of metabolic networks. Unfortunately, it is impossible to avoid thermodynamically infeasible loops in flux samples when using convex samplers on large metabolic models. Current strategies for randomly sampling the non-convex loopless flux space display limited efficiency and lack theoretical guarantees.

Results

Here, we present LooplessFluxSampler, an efficient algorithm for exploring the loopless mass-balanced flux solution space of metabolic models, based on an Adaptive Directions Sampling on a Box (ADSB) algorithm. ADSB is rooted in the general Adaptive Direction Sampling (ADS) framework, specifically the Parallel ADS, for which theoretical convergence and i

SUBMITTER: Saa PA 

PROVIDER: S-EPMC10763395 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature