Modeling Biology using Generic Reactive Animation

Complex biological systems involve incorporated behaviors of numerous processes, mechanisms and objects. However, experimental analysis, by its nature, divides biological systems into static interactions with little dynamics. To bridge the gap between experimental data and the underlying behavior, our group has been formalizing biological findings into mathematically and algorithmically rigorous specifications, which are then compiled into reactive models. To realistically animate our models, we designed a generic architecture for the earlier idea of reactive animation, in a way that allows it to link up reactive models with animation tools. Here, we describe the reactive animation approach and some of the benefits of employing it to simulate and analyze complex biological systems. We illustrate our approach with a model of pancreatic development, a highly complex system with a unique 3D structure, and also mention more recent work on adding animation to the generic cell project (GemCell). ∗Address for correspondence: Computational Science Lab, Microsoft Research, Cambridge, UK This research was supported in part by The John von Neumann Minerva Center for the Development of Reactive Systems, and by a grant from the Kahn Fund for Systems Biology, both at the Weizmann Institute of Science. Part of this David Harel’s work carried out during a visit to the School of Informatics at the University of Edinburgh, which was supported by a grant from the EPSRC. 2 Y. Setty et al. / Modeling Biology using Generic Reactive Animation