PolyRound: polytope rounding for random sampling in metabolic networks

Bioinformatics, vol. 38, pp. 566–567

Abstract

SUMMARY: Random flux sampling is a powerful tool for the constraint-based analysis of metabolic networks. The most efficient sampling method relies on a rounding transform of the constraint polytope, but no available rounding implementation can round all relevant models. By removing redundant polytope constraints on the go, PolyRound simplifies the numerical problem and rounds all the 108 models in the BiGG database without parameter tuning, compared to ∼50% for the state-of-the-art implementation. AVAILABILITY AND IMPLEMENTATION: The implementation is available on gitlab: https://gitlab.com/csb.ethz/PolyRound. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors 4

1. Axel Theorell corresponding

   SIB Swiss Institute of Bioinformatics · Forschungszentrum Jülich

   Affiliation as printed

   Department of Biosystems Science and Engineering, SIB Swiss Institute of Bioinformatics , 4058 Basel, Switzerland

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52425 Jülich, Germany

2. Johann F. Jadebeck Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52425 Jülich, Germany

3. Katharina Nöh

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52425 Jülich, Germany

4. Jörg Stelling corresponding

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   Department of Biosystems Science and Engineering, SIB Swiss Institute of Bioinformatics , 4058 Basel, Switzerland