Statecharts: A visual formalism for complex systems
Science of Computer Programming
On the development of reactive systems
Logics and models of concurrent systems
Object-oriented analysis and design with applications (2nd ed.)
Object-oriented analysis and design with applications (2nd ed.)
The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts
HCC '01 Proceedings of the IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC'01)
Formally specifying t cell cytokine networks with b method
CIS'04 Proceedings of the First international conference on Computational and Information Science
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
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Remarkable progress in various fields of biology is leading in the direction of a complete map of the building blocks of biological systems. There is broad agreement among researchers that 21st century biology will focus on attempting to understand how component parts collaborate to create a whole. It is also well agreed that this transition of biology from identifying the building blocks (analysis) to integrating the parts into a whole (synthesis) should rely on the language of mathematics. In a recent publication, we described the results of a first attempt at confronting the above challenge using the visual formalism of statecharts. We presented a detailed model for T cell activation using statecharts within the general framework of object-oriented modeling. In this work, we compare the statechart-based modeling approach to a Boolean formalism presented by Thomas & D'Ari. This comparison was done by taking a model for T cell activation and anergy, which was constructed by Kaufman et al. using such a Boolean formalism, and translating it into the language of statecharts. Comparing these two representations of the same phenomena allows us to assess the advantages and disadvantages of each modeling approach. We believe that the results of this work, together with the results of our previous modeling work on T cell activation, should encourage the use of visual formalisms such as statecharts for modeling complex biological systems. A full version of this paper appeared in the proceedings of the Second International Conference on Systems Biology, Pasadena, CA, USA, 2001 [9].