Parsing and Model Generation for Biological Processes

LAOUEN BELLOLI; GABRIEL WAINER; RAFAEL NAJMANOVICH

Pasadena, CA

Simposio; 2016 Symposium on Theory of Modeling and Simulation (TMS-DEVS); 2016

Society for Modeling & Simulation International ( SCS )

Modelling allows us to focus on the important components of a system under study, leaving aside the non-meaningful information. To study metabolic networks, we need to create a new model of the phenomena in order to start the simulations. Here, we propose a method for automating model-ing and simulation of biological cell processes using DEVS. We have built a parser and a model-generator in order to read SBML files and generate the model from the data. We also defined a generic model container for a biological cell including essential attributes of a cell, which can be instantiated using SBML to generate individual models.