A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools.

A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools.

Comput Biol Med. 2018 Dec 17;105:64-71

Authors: Rawls KD, Dougherty BV, Blais EM, Stancliffe E, Kolling GL, Vinnakota K, Pannala VR, Wallqvist A, Papin JA

Abstract
GEnome-scale Network REconstructions (GENREs) mathematically describe metabolic reactions of an organism or a specific cell type. GENREs can be used with a number of constraint-based reconstruction and analysis (COBRA) methods to make computational predictions on how a system changes in different environments. We created a simplified GENRE (referred to as iSIM) that captures central energy metabolism with nine metabolic reactions to illustrate the use of and promote the understanding of GENREs and constraint-based methods. We demonstrate the simulation of single and double gene deletions, flux variability analysis (FVA), and test a number of metabolic tasks with the GENRE. Code to perform these analyses is provided in Python, R, and MATLAB. Finally, with iSIM as a guide, we demonstrate how inaccuracies in GENREs can limit their use in the interrogation of energy metabolism.

PMID: 30584952 [PubMed - as supplied by publisher]