Computational Methods in Systems Biology: First by Amitai Regev, Ehud Shapiro (auth.), Corrado Priami (eds.)

By Amitai Regev, Ehud Shapiro (auth.), Corrado Priami (eds.)

This booklet constitutes the refereed court cases of the overseas Workshop on Computational equipment in platforms Biology, CMSB 2003, held in Rovereto, Italy, in February 2003.

The eleven revised complete papers offered including 2 invited papers, 7 place papers, and eleven abstracts have been rigorously reviewed and chosen from 30 submissions. one of the issues addressed are modeling languages for platforms biology, concurrency in organic structures, constraint programming, logical equipment in structures biology, formal equipment for the research of biomolecular structures, quantitative research of biomolecular platforms, and simulation and modeling options for platforms biology.

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Extra resources for Computational Methods in Systems Biology: First International Workshop, CMSB 2003 Rovereto, Italy, February 24–26, 2003 Proceedings

Example text

Complexes are drawn by connecting two-by-two bound sites of proteins, thus building connected graphs such as: 3 A 1 1 2 3 B C 2 1 2 which represents a compound made of A, B, and C, where A is connected with B and C, and there is no direct connection between B and C. Other examples of complexes are: 3 4 1 A 3 2 a self−complexation A 2 3 1 B 3 2 D 2 1 1 4 a ring−complex C A 2 3 2 1 1 4 4 3 B 2 1 a double contact Graphs for Core Molecular Biology 37 Solutions and Reactions. Solutions are multisets of proteins and complexes.

28 [22] A. Regev, W. Silverman, and E. Shapiro. Representation and simulation of biochemical processes using the π-calculus process algebra. In Pacific Symposium of Biocomputing (PSB2001), pages 459–470, 2001. 21, 29, 31 Graphs for Core Molecular Biology Vincent Danos1 and Cosimo Laneve2 1 2 ´ Equipe PPS, CNRS and University of Paris 7 Department of Computer Science, University of Bologna Abstract. A graphic language—the graphic κ calculus—modeling protein interactions at the domain level is introduced.

Knapp, K. Laderoute, P. Lincoln, J. Meseguer, and K. Sonmez. Pathway logic: Simbolic analysis of biological signaling. In Proceedings of the Pacific Symposium on Biocomputing, pages 400–412, 2002. 21, 32 [6] D. Endy and R. Brent. Modelling cellular behaviour. Nature, 409:391–395, 2001. 21, 32 [7] G. Fournet and G. Gonthier. The reflexive chemical abstract machine and its join calculus. In Proc. 23rd ACM POPL, pages 372–385, 1996. [8] P. J. E. Goss and J. Peccoud. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets.

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