Efficient Discovery of Genome-scale Metabolic Pathways for Synthetic Biology

Implementation of the computational method kOpt, corresponding to the manuscript "Efficient Discovery of Genome-scale Metabolic Pathways for Synthetic Biology".

Abstract

Motivation: Genome-scale metabolic networks and metabolic networks extended by new-to-nature reactions exceed the practical size of enumerating elementary flux modes, yet such enumeration is required to take advantage of the networks. Results: A novel method, called kOpt, was developed and implemented to compute the first k flux solutions having increased flux pattern variability for reactions close to the product in the stoichiometric reaction network. The novel method proved feasible for genome-scale metabolic networks and compared favourably to a method enumerating the first k elementary flux modes. More specifically, the proposed method was approximately two orders of magnitude faster and yielded a more varied set of solutions.

Contents

• README.md

  This file

• kOPt

  This folder contains the MATLAB implementation of the kOPt method. Two versions of the code ara available, with the difference that one uses cplex for the optimization process and the second one can be used with GLPK optimization software.

• kOptResults

  The results for each of the networks is stored in a separate mat file. The structure contains the optimization Objective values, running times, flux solutions and binary values of the flux solutions for optimization round.

• EFMs

  The results for the enumeration of EFMs method. The running times and obtained EFMs for each network are saved in separate files.

• EFMsResults

• data

The data folder stores the stoichiometric (S) matrices representing the metabolic networks that we have used in the project. The S matrices are organized such that the rows represent metabolites, and the columns correspond to reactions in the network.

• figures

  Matlab code for generation of the figures, and figures in different formats.

• calculateVariation

  Scripts for calculation of the variability of the obtained solutions.

• supplementaryScripts

  Additional scripts required either for the methods or for the figure generation.