Investigating embryogenesis using numerical simulations of biophysics
Ivo Sbalzarini (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany)
Development and morphogenesis of tissues, organs, and embryos emerges from the collective self-organization of cells that communicate though chemical and mechanical signals. Decisions about growth, division, and migration are taken locally by each cell based on the collective information. In this sense, a developing tissue is akin to a massively parallel computer system, where each cell or processor computes robust local decisions, integrating communication with other cells/processors. Mechanistically understanding and reprogramming this system is a grand challenge. Our vision is to develop a virtual computer model of a developing embryo, incorporating the known biochemistry and biophysics into a computational model in 3D-space and time, in order to understand the information-processing aspects of development on an algorithmic basis. While the “hardware” (proteins, lipids, etc.) and the “source code” (genome) are increasingly known, we known virtually nothing about the algorithms that this code implements on this hardware. Using examples from our work, I outline our roadmap toward a virtual embryo, and highlight challenges along the way. These range from globally optimal approaches to image analysis, to novel languages for parallel high-performance computing, to virtual reality and real-time graphics for 3D microscopy and numerical simulations of biochemical and biomechanical models. This cooperative interdisciplinary effort contributes to all involved disciplines.
Ivo Sbalzarini is the Chair of Scientific Computing for Systems Biology on the faculty of computer science of TU Dresden, and director of the TUD-Department in the Center for Systems Biology Dresden. He also is a permanent Senior Research Group Leader with the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden. He graduated in Mechanical Engineering from ETH Zurich in 2002 (Willi Studer Award). He completed his doctorate in computer science in 2006 at ETH Zurich (Chorafas Award, Weizmann Institute of Science), where he formed a close collaboration between biology and computer science. In 2006, he was named Assistant Professor for Computational Science in the Department of Computer Science of ETH Zurich. In 2012, Ivo and his group moved to Dresden, where he became one of the founding members of the new Max Planck Center for Systems Biology and the TU-Dresden Chair of Scientific Computing for Systems Biology. He also serves as a co-leader of the biological systems path of the Center for Advancing Electronics Dresden, Dean of the International Max Planck Research School in Cell, Developmental, and Systems Biology, and Vice-Dean of the Faculty of Computer Science.