Formal Methods for Computational Systems Biology: 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2008 Bertinoro, Italy, June 2-7, 2008
Marco Bernardo, Pierpaolo Degano, Gianluigi Zavattaro
Springer Science & Business Media, 20.05.2008 - 527 Seiten
This volume presents the set of papers accompanying the lectures of the eighth International School on Formal Methods for the Design of Computer, Com- nication, and Software Systems (SFM). Thisseriesofschoolsaddressestheuseofformalmethodsincomputerscience asaprominentapproachtotherigorousdesignofcomputer, communication, and software systems. The main aim of the SFM series is to o'er a good spectrum of current research in foundations as well as applications of formal methods, which can be of help for graduate students and young researchers who intend to approach the ?eld. SFM 2008 was devoted to formal techniques for computational systems - ology and covered several aspects of the ?eld, including computational models, calculi and logics for biological systems, and veri'cation and simulation me- ods. Theschoolfeatured not onlyregularlectures, but also talksgivenby people involvedinthe ItalianresearchprojectonBio-InspiredSystems andCalculiwith Applications (BISCA). The ?rst partof this volume comprises nine papers basedon regularlectures. The paper by Degasperi and Gilmore describes the application of sensitivity analysistechniques to stochastic simulation algorithms. Talcott's paper presents pathway logic, an approach to modeling and analysis of biological processes based on rewriting logic. Fages and Soliman study reaction graphs and acti- tion/inhibition graphs used by biologists through formal methods originating from programming theory. The paper by Maus, John, R] ohl, and Uhrmacher d- cusses categories, abstraction hierarchies, and composition hierarchies playing a role in modeling and simulation for computational biology. Gillespie's paper - views the theory of stochastic chemical kinetics and several simulation methods that are based on that theory.
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Sensitivity Analysis of Stochastic Models of Bistable Biochemical Reactions
Formal Cell Biology in Biocham
Hierarchical Modeling for Computational Biology
Simulation Methods in Systems Biology
Membrane Computing as a Modeling Framework Cellular Systems Case Studies
Petri Nets for Systems and Synthetic Biology
Process Algebras in Systems Biology
A Holistic Approach
The Calculus of Looping Sequences
Hybrid Systems and Biology Continuous and Discrete Modeling for Systems Biology
A πBased Process Calculus for the Implementation of Compartmentalised Bioinspired Calculi
A Gentle Introduction to Stochastic PolyAutomata Collectives and the BioChemical Ground Form
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Formal Methods for Computational Systems Biology: 8th International School ...
Marco Bernardo,Pierpaolo Degano,Gianluigi Zavattaro
Eingeschränkte Leseprobe - 2008
abstract action activation algorithm allows ambient analysis application approach approximation associated behaviour binder binding biochemical biological bound calculus called cell channel checking chemical communication compartment complex components composition Computing concentration condition consider constant contains continuous corresponding cytoplasm deﬁned deﬁnition derived described diﬀerent discrete dynamics elements encoding enzyme equation event example expression extension Figure ﬁrst formal function gene given glucose graph hybrid initial interaction introduced involved kinetic label language LNCS logic means membrane method molecular molecules multiset networks objects obtained occur operator output parameters pathway perform Petri ports possible present properties protein reactants reaction relation represent representation respectively rewrite rules semantics sequence signal silico simulation species speciﬁc Springer step stochastic structure term transition values variables