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Visual programming for modeling and simulation of biomolecular regulatory networks. (English) Zbl 1032.68810

Sahni, Sartaj (ed.) et al., High performance computing - HiPC 2002. 9th international conference, Bangalore, India, December 18-21, 2002. Proceedings. Berlin: Springer. Lect. Notes Comput. Sci. 2552, 702-712 (2002).
Summary: In this paper we introduce our new tool BIOSKETCHPAD that allows visual progamming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks using a menu of icons, arrows, and pop-up menus, and translates the input model into CHARON, a modeling language for modular design of interacting multi-agent hybrid systems. Hybrid systems are systems that are characterized by continuous as well as discrete dynamics. Once a CHARON model of the underlying system is generated, we are able to exploit the various analysis capabilities of the CHARON toolkit, including simulation and reachability analysis. We illustrate the advantages of this approach using a case study concerning the regulation of bioluminescence in a marine bacterium.
For the entire collection see [Zbl 1014.00025].

MSC:

68U20 Simulation (MSC2010)
92B99 Mathematical biology in general
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