In silico analysis of steady state mechanisms of metabolic networks in COBRA Toolbox and FBA-SimVis
2011
Odzina, I., Latvia Univ. of Agriculture, Jelgava (Latvia) | Pentjuss, A., Latvia Univ. of Agriculture, Jelgava (Latvia)
Metabolic analysis is one of the research focuses of systems biology. Two aspects of metabolic networks -network topology and stoichiometry - are what current researchers are most interested in, and both studies have revealed significant information. The research of the stoichiometric matrix of metabolic network has generated a series of powerful methodologies such as flux balance analysis (FBA). For FBA different methods execution are used different software like COBRA Toolbox and FBA-SimVis. The aim of this paper is to compare and analyze functionality of these two toolboxes, metabolic network data conformation conditions, and to compare all available FBA methods comparison in calculation possibilities and visual interpretation way. FBA, when analyzing all fluxes using different options, gives results in its metabolic network flow chart, although Cobra Toolbox returns the results in the matrix in number formats. FBA-SimVis for Steady state metabolic network models analysis is provided for a small metabolic network, because making some FBA analysis there are a ten possibilities to change an unlimited count of variables, to choose or change or optimize reactions as variables. Cobra Toolbox for Steady state metabolic network models analysis is provided for greater metabolic networks with hundreds or thousands of reactions. It allows changing an unlimited count manipulating and optimizing reactions fluxes.
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