The Whole Organism Modeling Project

David Harel
David Harel
The Weizmann Institute of Science, Israel
November 21 2013 13:30~14:45


The talk shows how techniques from computer science and software engineering can be applied beneficially to research in the life sciences. We discuss the idea of comprehensive and realistic modeling of biological systems, where we try to understand and analyze an entire system in detail, utilizing in the modeling effort all that is known about it. I will address the motivation for such modeling and the philosophy underlying the techniques for carrying it out, as well as the crucial question of when such models are to be deemed valid, or complete. The examples will be from among the biological modeling efforts my group has been involved in: T cell development, lymph node behavior, organogenesis of the pancreas, rat whisking, cancer tumor formation, and fate determination in the reproductive system of the C. elegans nematode worm. The ultimate long-term “grand challenge” is to produce an interactive, dynamic, computerized model of an entire multi-cellular organism, such as the C. elegans, which is extremely complex despite its small size, but well-defined in terms of anatomy and genetics.


Research Interests

In the past Harel worked in several areas of theoretical computer science, including computability theory, logics of programs, database theory, and automata theory. Over the years, his activity in these areas diminished, and he has become involved in several other areas, including software and systems engineering, object-oriented analysis and design, visual languages, layout of diagrams, modeling and analysis of biological systems, and the synthesis and communication of smell. As part of these interests, he has put forward three grand challenges: for liberating programming, for modeling an entire multi-cellular organism, and for a system of odor communication and synthesis. Harel is the inventor of the language of Statecharts, and co-inventor of Live Sequence Charts, Reactive Animation, and Behavioral Programming. He was part of the team that designed the tools Statemate, Rhapsody the Play-Engine and PlayGo.


Awards and Honors

  • Book of the Year Award, Addison-Wesley UK, 1987.
  • Best Paper Award, 10th Int’l Conf. on Software Engineering,1988.
  • Spring Main Book Selection, Macmillan Library of Science, 1988.
  • ACM Karlstrom Outstanding Educator Award, 1992.
  • Fellow, ACM, 1994.
  • Fellow, IEEE, 1995.
  • Stevens Award in Software Development Methods, 1996.
  • Most Influential Paper Award, 20th Int’l Conf. on Software Engineering, 1998.
  • Best Paper Award, IEEE Symp. on Visual Languages and Formal Methods, 2001.
  • Israel Prize, 2004.
  • Doctor Honoris Causa, University of Rennes, France, 2005.
  • Fellow Honoris Causa, Open University of Israel, 2006.
  • Member, Academia Europaea, 2006.
  • ACM SIGSOFT Outstanding Research Award, 2006.
  • Doctor (Laura) Honoris Causa, University of Milano–Bicocca, Italy, 2007.
  • Fellow, AAAS, 2007.
  • ACM Software System Award, 2007.
  • ACM SIGSOFT Impact Paper Award, 2008.
  • Member, Israel Academy of Sciences and Humanities, 2010.
  • Eme”t Prize, 2010.
  • Doctor Honoris Causa, Eindhoven Univ. of Technology, The Netherlands, 2012.
  • ABZ Platinum Gold Medal for CS and CS Education, ETH Zurich, 2013.
  • Most Influential Paper Award, VL/HCC, 2012.