Transactions on Computational Systems Biology XII

Transactions on Computational Systems Biology XII

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Inspired by the interesting contributions to the 6th Conference on Compu- tional Methods in Systems Biology (CMSB 2008) and the Dagstuhl Seminar 09091ona€œFormalMethods inMolecular Biologya€inFebruary2009, papershave been selected for this special issue of the journal TransactionsonComputational Systems Biology, under the title Modeling Methodologies. The special issue starts with a position paper on a€œBiomodel Engineering a€“ from Structure to Behaviora€, which discusses the potential that concepts from traditional computing science hold for creating more powerful models of biol- ical systems and identi?es venues for challenging future research. The technical contributions of the special issue covera broadrangeof mod- ing methodologies that have recently been developed in computational systems biology. First, twonewmodelinglanguagesarepresented.Thea€œAttributed?-Calculus withPrioritiesa€presentsacombinationofaconcurrentprocesslanguage, i.e., the ?-calculus, and a sequential core language, i.e., the ?-calculus; being equipped withprioritiesthelanguageenablesthedescriptionofdiversespatialphenomena, di?erent kinetics, as well as an individual-based and population-based modeling of biological systems. It is shown how the di?erent dialects of the ? calculus, including the pi@-calculus, can be expressed. Its stochastic semantic is ?rmly rooted in CMTC's and is re?ected in the stochastic simulator.Versari, C., Busi, N.: Stochastic simulation of biological systems with dynamical compartment structure. In: Calder, M., Gilmore, S. (eds.) ... PhD thesis, Universit Ie des Sciences et Technologies de Lille - Lille 1 (2007) 28. Versari, C.: A Coreanbsp;...

Title:Transactions on Computational Systems Biology XII
Author:Corrado Priami, Rainer Breitling, David Gilbert, Monika Heiner, Adelinde M. Uhrmacher
Publisher:Springer Science & Business Media - 2010-02-18


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