Concurrency in Biological Modeling: Behavior, Execution and Visualization

David Harel, Yaki Setty, Sol Efroni, Naamah Swerdlin, Irun R. Cohen

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Modeling natural systems is a complicated task that involves the concurrent behavior of various processes, mechanisms and objects. Here, we describe an approach that we have been taking in our group for several years, whereby the complexity of the problem is reduced by decomposing a natural system into its basic elements, which are then reassembled and combined to form a comprehensive, simulatable model of the system. Our modeling approach allows one to view a natural system at various levels of abstraction, in a way that makes it possible to zoom in and out between levels. Using statecharts, a high level visual formalism, we specify the behavior of the basic elements of each level and compile these into executable code, which is then linked to an animated front-end. At run-time, the concurrent execution of the basic elements is continuously displayed and provides a dynamic description of the system. We illustrate this approach by modeling aspects of three biological systems: development of the mammalian pancreas; the differentiation of T cells in the thymus; and the dynamic architecture of a lymph node. We compared each model's behavior with experimental data and also reproduced genetic experiments in silico. Interestingly, certain behavioral properties that were not explicitly programmed into the model emerge from concurrent execution and correspond well with the experimental observations.

Original languageEnglish
Pages (from-to)119-131
Number of pages13
JournalElectronic Notes in Theoretical Computer Science
Issue number3
StatePublished - 20 Jan 2008
Externally publishedYes

Bibliographical note

Funding Information:
1 Part of this author’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 Email: 3 Email: 4 Email: 5 Email: 6 Email: 7 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.


  • Reactive Animation
  • biological modeling
  • concurrent modeling
  • reactive systems
  • statecharts


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