A 3D Multicellular Simulation Layer for the Synthetic Biology CAD Infobiotics Workbench Suite

Abstract

Although computational solutions are commonplace in Synthetic Biology laboratories that use software, proprietary or otherwise, the use of multicellular simulations promises to enhance such workflows by in silico prototyping via spatiotemporal biological simulations prior to the in vitro genetic manipulation of cell lines. Thus, a multicellular layer for the Infobiotics Workbench Synthetic Biology platform was pursued with a view towards impactful multicellular case studies. This work interrogates and benchmarks a variety of multicellular modalities, including the application of parallel subcellular stochastic simulations for computing biochemical network models. Phenotypic and microenvironmental characteristics were meticulously reviewed to effectively construct the multicellular designs that could elicit emergent population level consequences. The result was the benchmarking of a batch processed solution compared to one utilizing Unreal Engine 4 in real time, along with the elucidation of relative characteristics and performances. Such simulations proved very computationally intensive as prototyped on conventional hardware, hence this work alluded to the need for high performance computing especially regarding biochemical parallelization.