Team:IISER-Bhopal-India/Model

Team Methnote

Modeling

Flux balance analysis and model building

Simulating optimal growth using flux balance analysis (FBA) is one of the fundamental COBRA phenotypic calculations for metabolic network models of an organism. It is a method that used to calculate the flow of metabolites through a metabolic network. The COBRA Toolbox supports models in the Systems Biology Markup Language (SBML) format. The COBRA-compilant SBML file is organism specific and can be downloaded from literature. Growth is stimulated by optimizing the model for flux through the model’s biomass reaction which is set as an objective function however, it is also possible to perform simulations that focus on optimizing other biological characteristics, such as ATP production.

We have been trying to do FBA of our chassis organism P. pastoris. We intend to introduce the sMMO pathway in the existing metabolic model of our chassis. FBA is being done for P. pastoris with the sMMO complex catalyzed reaction added to its metabolism in the corresponding COBRA-compilant SBML file for P. pastoris. Simulated optimal growth if obtained, validates the model to a considerable extent and helps in optimizing growth conditions for the organism.

Apart from this the model building for metabolic reactions in P. pastoris is being done using the simbiology toolbox in matlab.