Using Design Patterns in Scientific Applications: A Case Study in CompuCell3D

Revision with unchanged content. Design Patterns have been widely adopted for building flexible and extensible applications. However, this can come at a cost of reduced performance, which may not be acceptable for computationally intensive scientific applica­tions. Therefore, the effects of design patterns on application performance are investigated through a detailed measurement and profiling of CompuCell3D. It is a software framework for three-dimensional modeling (3D) of morpho­genesis, which is a stage in embryonic development where cells cluster into tissues and organs. By reverse engineering CompuCell3D subsystems with and without design patterns, their impact on application performance and­maintainability is evaluated. Finally, CompuCell3D functionality is extended to support irregular domains for biologically realistic simulations.