influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments.

ABSTRACT

MOTIVATION The problem of stationary metabolic flux analysis based on isotope labelling experiments first appeared in the early 1950s and was basically solved in early 2000s. Several algorithms and software packages are available for this problem. However, the generic stochastic algorithms (simulated annealing or evolution algorithms) currently used in these software require a lot of time to achieve acceptable precision. For deterministic algorithms, a common drawback is the lack of convergence stability for ill-conditioned systems or when started from a random point. RESULTS: In this article, we present a new deterministic algorithm with significantly increased numerical stability and accuracy of flux estimation compared with commonly used algorithms. It requires relatively short CPU time (from several seconds to several minutes with a standard PC architecture) to estimate fluxes in the central carbon metabolism network of Escherichia coli. AVAILABILITY: The software package influx_s implementing this algorithm is distributed under an OpenSource licence at http//metasys.insa-toulouse.fr/software/influx/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.