Spatial Modeling Tools for Cell Biology

Abstract : Rapid accumulation of genomic and proteomic data from novel high throughput experimental screening technologies demand novel mathematical approaches and models to process and interpret massive amounts of data. Scientific potentials and military relevance of computational biology and bioinformatics have inspired DARPA/IPTO's visionary BioSPICE project to develop computational framework and modeling tools for cell biology. The goal of this CFDRC project was to formulate fundamental mathematical models and their numerical solution procedures for solving spatiotemporal cell biology problems and to develop software tools for multi-dimensional modeling of cell and tissue biology. CFDRC has developed Computational Biology, CoBi, software tools to simulate complex cell and organ biology problems. The code has been successfully applied to a number of cell biology problems including: bacterial chemosensing and chemotaxis, bacterial sporulation, EGFR signal transduction, cellular and tissue calcium oscillations, cellular and tissue oxygen and energy metabolism, morphogenesis of the yeast cell, and perfusion of a cell in an organ.