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.

One of the biodiesel production problems is occurrence of a significant quantity (about 10%) of the by-product – glycerol. This problem is offered to solve by adaptation of bacteria Zymomonas mobilis, which is notable for ethanol production facilities. To be able to process glycerine into ethanol using Z.mobilis bacteria, the bacteria must be modified. At the same time, computer modelling analysis is required to assess specific modification affectivity in interconnection with other processes in bacteria. Computer model results of simulated experiment to understand and predict that the cells and biological processes are essential to reduce the number of experiments. This in turn reduces the necessary financial resources and time, bio-medical biotechnology, pharmaceutical and environmental problems. The model describes conversion of glycerol into bioethanol in Z.mobilis bacterial cell. First phase of model creation is creation of a structure model based on biochemical reactions using computer software CellDesigner. On the second phase of model creation, kinetic parameters which are available in literature were identified. Using the databases KEGG, SABIO-RK, BRENDA, reactants, kinetic parameters and reaction equation types were defined. Dynamic model of Z. mobilis biochemical network was created using computer software Copasi. The dynamic model describes conversion of glycerol into bioethanol in Z.mobilis bacterial cell. In this time simulation data of the computer model of natural organisms are not to confirm laboratory experimental data. Simulation data of the computer model are not correct to prevent this problem is required parameter estimation in computer software COPASI.