Reactive animation: From piecemeal experimentation to reactive biological systems

Abstract

Over the past decade, multi-level complex behavior and reactive nature of biological systems, has been a focus point for the biomedical community. We have developed a computational approach, termed Reactive Animation (RA) for simulating such complex biological systems. RA is an approach for describing the dynamic characteristics of biological systems based on facts collected from experiments. These data are integrated bottom-up by computational tools and methods for reactive systems development and are simulated concomitantly to a front-end user friendly visualization and reporting systems. Using RA, the experimenter may intervene mid-simulation, suggest new hypotheses for cellular and molecular interactions, apply them to the simulation and observe their resulting outcomes “on-line”. Several RA models have been developed including models of T cell activation, thymocyte development and pancreatic organogenesis, which are describe in the in this review.

Keywords::

• Reactive animation
• complex systems
• computational models
• systems biology
• statecharts
• simulation
• thymus
• pancreas
• T cell activation

Acknowledgements

David Harel is the William Sussman Professor in the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science. Irun R. Cohen is Professor of Immunology, Emeritus at the Weizmann Institute of Science. Sol Efroni and Oded Vainas are at the Mina and Everard Goodman Faculty of Life Science, Bar Ilan University.

Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.