(369a) SMBLtoODEpy: A Software Program for Converting SBML Models into ODE Models in Python | AIChE

(369a) SMBLtoODEpy: A Software Program for Converting SBML Models into ODE Models in Python


Ruggiero, S. M. - Presenter, Oklahoma State University
Ford Versypt, A. N., Oklahoma State University
Systems Biology Markup Language (SBML) is a standard intermediate language for representing models of biological systems, particularly reaction networks. SBML defines models independent of the software used to create the model, which allows for easy import and export of models. Programs for converting models into code exist for a variety of software languages but have key limitations. This work seeks to address these limitations by enabling conversion of SBML models into Python classes that can be rapidly incorporated into biomedical systems modeling projects written in Python, including the multiscale simulation platform CompuCell3d, which defines continuum fields via Python. The software program developed is called SMBLtoODEpy. The program aims to accelerate construction of multiscale models that import and reuse published SBML models, many of which are available in the BioModels Database available at https://www.ebi.ac.uk/biomodels/

In SMBLtoODEpy, each of the model components are retrieved using libSBML, a software library for parsing and editing SBML models. The model components are output to a text file is formatted to be easier to edit than either the SBML or Python implementations of the model. Then, the generated text file is used to create a Python file. The generated Python class is based on a template ODE model. This template ensures a standard interface between the ODE model and other components in a multiscale model. We will demonstrate the use of the SBMLtoODEpy program for multiple case studies as a verification of its functionality.