David Harel
Dept. of Computer Science and Applied Math.
Weizmann Institute
Rehovot, Israel
Biological Systems as Reactive Systems
Abstract
The course shows the way software and systems engineering, especially of reactive systems, can be applied beneficially to the life sciences. I will discuss the idea of comprehensive and realistic computerized modeling of biological systems. In comprehensive modeling the main purpose is to understand an entire system in detail, utilizing in the modeling effort all that is known about the system, and to use that understanding to analyze and predict behavior in silico. In realistic modeling the main issue is to model the behavior of actual elements, making possible totally interactive and modifiable realistic executions/simulations that reveal emergent properties. 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. In our work we have used visual formalisms, such as statecharts and live sequence charts, for the modeling, and powerful execution and analysis tools to back these up. The lectures will describe these as well as several actual examples from among the biological modeling efforts my group has been involved in: T cell development in the thymus, lymph node behavior, embryonic development of the pancreas, the C. elegans reproductive system, and a generic cell model. Time permitting, I will also discuss a new concept we have recently proposed to replace the classical notion of a gene.
Course materials
- D. Harel. Biological systems as reactive systems. Lecture slides [part1.ppt, part2.ppt, part3.ppt, part4.ppt, password-protected].
- D. Harel. On comprehensive and realistic modeling: some ruminations on the what, the how and the why. Clin. and Invest. Med., v. 28, n. 6, pp. 334-337, 2005.
- D. Harel. A grand challenge for computing: towards full reactive modeling of a multi-cellular animal.
- J. Fisher, N. Piterman, E. J. A. Hubbard, M. J. Stern, D. Harel. Computational insights into Caenorhabditis elegans vulval development. Proc. of Nat. Acad. of Sci., v. 102, n. 6, pp. 1951-1956, 2005.
- S. Efroni, D. Harel, I. R. Cohen. Towards rigorous comprehension of biological complexity: modeling, execution, and visualization of thymic T-cell maturation. Genome Research, v. 13, pp. 2485-2497, 2003.
- S. Efroni, D. Harel, I. R. Cohen. Emergent dynamics of thymocyte development and lineage determination. PLoS Comput. Biol., v. 3, n. 1, paper e13, 2007.
- D. Harel. A Turing-like test for biological modeling. Nature Biotechn., v. 23, n. 4, pp. 495-496, 2005.
- E. Fox Keller, D. Harel. Beyond the gene. PLoS ONE, v. 2, n. 11, paper e1231, 2007.
- D. Harel. Can programming be liberated, period? IEEE Computer, v. 41, n. 1, pp. 28-37, 2008.
- H. Amir-Kroll, A. Sadot, I. R. Cohen, D. Harel. GemCell: a generic platform for modeling multi-cellular biological systems. Theor. Comput. Sci., v. 391, n. 3, pp. 276-290, 2008.
Last changed
March 12, 2008 23:54 EET
by
local organizers, ewscs08(at)cs.ioc.ee
EWSCS'08 page:
//cs.ioc.ee/ewscs/2008/