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APLAS
2007
ACM

Scalable Simulation of Cellular Signaling Networks

10 years 10 months ago
Scalable Simulation of Cellular Signaling Networks
Abstract. Given the combinatorial nature of cellular signalling pathways, where biological agents can bind and modify each other in a large number of ways, concurrent or agent-based languages seem particularly suitable for their representation and simulation [1,2,3,4]. Graphical modelling languages such as [5, 6, 7, 8], or the closely related BNG language [9,10,11,12,13,14], seem to afford particular ease of expression. It is unclear however how such models can be implemented.1 Even a simple model of the EGF receptor signalling network can generate more than 1023 non-isomorphic species [5], and therefore no approach to simulation based on enumerating species (beforehand, or even on-the-fly) can handle such models without sampling down the number of potential generated species. We present in this paper a radically different method which does not attempt to count species. The proposed algorothm uses a representation of the system together with a super-approximation of its `event horizon...
Vincent Danos, Jérôme Feret, Walter F
Added 12 Aug 2010
Updated 12 Aug 2010
Type Conference
Year 2007
Where APLAS
Authors Vincent Danos, Jérôme Feret, Walter Fontana, Jean Krivine
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