By Amitai Regev, Ehud Shapiro (auth.), Corrado Priami (eds.)
This e-book constitutes the refereed lawsuits of the foreign Workshop on Computational equipment in platforms Biology, CMSB 2003, held in Rovereto, Italy, in February 2003.
The eleven revised complete papers provided including 2 invited papers, 7 place papers, and eleven abstracts have been conscientiously reviewed and chosen from 30 submissions. one of the subject matters addressed are modeling languages for platforms biology, concurrency in organic structures, constraint programming, logical tools in structures biology, formal equipment for the research of biomolecular structures, quantitative research of biomolecular platforms, and simulation and modeling innovations for structures biology.
Read or Download Computational Methods in Systems Biology: First International Workshop, CMSB 2003 Rovereto, Italy, February 24–26, 2003 Proceedings PDF
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Extra info for Computational Methods in Systems Biology: First International Workshop, CMSB 2003 Rovereto, Italy, February 24–26, 2003 Proceedings
The free sites i, j, h and k are bound by the complexation rule, thus making “real” the virtual connection in the left hand side. Intuitively, virtual connectedness is a causality constraint saying that all reactions need to go through a temporary super complex for anything to happen. If not, then the reaction is not elementary in some sense and should be decomposed further. It might be interesting to study the restricted system with explicit temporary complexes but we don’t do this here. 38 Vincent Danos and Cosimo Laneve Firing a reaction.
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  D. Endy and R. Brent. Modelling cellular behaviour. Nature, 409:391–395, 2001. 21, 32  G. Fournet and G. Gonthier. The reﬂexive chemical abstract machine and its join calculus. In Proc. 23rd ACM POPL, pages 372–385, 1996.  P. J. E. Goss and J. Peccoud. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets.
In a way, our embedding is bringing to the fore a precise counterpart of the converse intuition, namely that protein interactions constitute a rudimentary process algebra. And therefore, we can reasonably expect this analysis to give means to import and adapt automatic tools already developed by process algebraists [2, 9, 15]. How relevant this could prove to be for the understanding of biological systems remains to be seen. Related Work. A language with quite similar concerns, but with an eye on applying rewriting theory rather than concurrency theory, called “Pathway Logic”, has been recently proposed by Lincoln and collaborators in .