Breathing Life into Mathematical Models of Biological Systems

Mathematical and computational models are becoming more prominent in biological and bioinformatics research. However, the designing, programming, testing and even utilization of computer models has not yet found the acceptance it deserves within the biological research community. Why is that? First, there seems to be a wide communication gap between how biologists think about biological systems and how computer scientists, bioinformaticians, and mathematical modelers implement their formal models of living systems. Second, visualization plays an immensely important role in promoting and communicating computational models beyond their mathematical formalisms. The visualization aspect, however, is usually ignored in the presentation of mathematical models. Recent advances in computer hardware and new programming methodologies (such as GPU programming) now make it possible to embrace agent-based, object-oriented and rule-based approaches for the modeling of biological systems on a wider scale. Agent-based models lend themselves to more comprehensive and more natural representations of biological entities. To illustrate this viewpoint, I will present a variety of models with visualization examples, that demonstrate our latest swarm intelligence-based approaches to explore gene regulatory systems, blood clotting, immune system processes, and bacterial ecosystems on various scales: from bodies to organs to cells to proteins. The models will show how mathematical models can be brought to life, so to speak, and how to make them interactive, accessible, and fun(!) to anybody with an interest in scientific research and education.