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Multiscale simulation using Compucell3D and the SBML ODE Solver library

Ryan Roper University of Washington

Authors

Ryan Roper

Abstract

Compucell3D (CC3D) is a flexible tool for multicellular modeling and simulation. While basic simulations can be defined using only an XML input file, CC3D also provides a Python interface to permit scripting access to its core functionality. This provides an additional level of sophistication by allowing users to manipulate and customize native CC3D functionality and also incorporate additional functionality from non-native libraries. To extend CC3D for multiscale (cellular-subcellular) modeling, we have generated Python bindings for the SBML ODE Solver library (SOSlib). This permits CC3D scripting access to two important functions of SOSlib: (1) reading SBML-formatted ODE model definitions and (2) numerically solving ODE models. We present some basic simulations that illustrate how two-way 'communication' between the cellular level (CC3D) and the subcellular level (SOSlib) can be implemented using Python input files. In other words, properties and behavior of intracellular biochemical networks are shown to vary as a function of conditions and properties at the cellular level and vice-versa. We provide some discussion of how this framework may be used to develop more sophisticated simulations of complex biological processes. In addition, we note technical issues and difficulties that may need to be addressed to create a truly cohesive multiscale simulation environment.