Designing Biological Simulation Models Using Formalism-Based Functional and Spatial Decompositions

One of the most daunting challenges confronting computational biologists is a problem that simulation developers in all disciplines face: the design of simulation code that can be easily understood and modified despite the complexity of the systems being modeled. To meet this challenge, the authors apply the discrete event system specification (DEVS), a general modeling formalism invented for the formal description of a wide range of systems that vary in time. Using DEVS, developers can address the complexity of a biological model by subdividing it into a hierarchy of simpler submodels. Hierarchical design is a well-known strategy for software development in general. But the question remains, what type of decomposition should be used? The authors use the upper levels of a hierarchy to separate different functions or algorithms, and then dedicate lower levels to the partitioning of space. To illustrate the approach, they present a DEVS-based model that captures the 3D self-assembly of vesicle clusters and their role in the propagation of information between nerve cells.