MathLetter #4, July 2009

MathModelica Systems Biology Add-on

Parallel to the release of MathModelica 2.1 a beta release of a new add-on for systems biology modeling will be released. The beta version will be made available for beta testing for those that have active MathModelica Premier Service.

The add-on will include import and export to the Systems Biology Markup Language (SBML), Metabolic Control Analysis (MCA), as well as wizards that help you create Modelica models using the BioChem library.

Model example

The BioModels database contains a few hundreds SBML models. One of the models available there is a cell division model presented in Modeling the cell division cycle: cdc2 and cyclin interactions by John J. Tyson. (Proc. Nati. Acad. Sci. USA Vol. 88, pp. 7328-7332, August 1991 Cell Biology). Using the SBML import functionality, the model has been imported to MathModelica and the resulting model is shown in the figure below.

The proteins cdc2 and cyclin form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. Simulation and analysis of the model show that the control system can operate in three modes: as a steady state with high maturation promoting factor activity, as a spontaneous oscillator, or as an excitable switch. The simulation results are shown in the figure below and correspond to Fig 3A from the Tysons original publication.

Customers with active MathModelica Premier Service can apply for a beta (pre release) version of the systems biology add-on. Please contact support@mathcore.com to do this.

The systems biology add-on will be presented in the paper Creating a Bridge between Modelica and the Systems Biology Community by Jan Brugård et. al at the Modelica Conference 2009 in Como, Italy, September 20 - 22 2009.