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E-raamat: 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

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  • Formaat: PDF+DRM
  • Sari: Lecture Notes in Computer Science 5016
  • Ilmumisaeg: 31-May-2008
  • Kirjastus: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • Keel: eng
  • ISBN-13: 9783540688945
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  • Formaat: PDF+DRM
  • Sari: Lecture Notes in Computer Science 5016
  • Ilmumisaeg: 31-May-2008
  • Kirjastus: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • Keel: eng
  • ISBN-13: 9783540688945
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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.
Part I: Regular Lectures
Sensitivity Analysis of Stochastic Models of Bistable Biochemical Reactions
1(20)
Andrea Degasperi
Stephen Gilmore
Pathway Logic
21(33)
Carolyn Talcott
Formal Cell Biology in Biocham
54(27)
Francois Fages
Sylvain Soliman
Hierarchical Modeling for Computational Biology
81(44)
Carsten Maus
Mathias John
Mathias Rohl
Adelinde M. Uhrmacher
Simulation Methods in Systems Biology
125(43)
Daniel T. Gilespie
Membrane Computing as a Modeling Framework. Cellular Systems Case Studies
168(47)
Gheorghe Paun
Francisco Jose Romero-Campero
Petri Nets for Systems and Synthetic Biology
215(50)
Monika Heiner
David Gilbert
Robin Donaldson
Process Algebras in Systems Biology
265(48)
Federica Ciocchetta
Jane Hillston
The BlenX Language: A Tutorial
313(53)
Lorenzo Dematte
Corrado Priami
Alessandro Romanel
Part II: BISCA Talks
Cells in Silico: A Holistic Approach
366(21)
Davide Chiarugi
Pierpaolo Degano
Jan Bert Van Klinken
Roberto Marangoni
The Calculus of Looping Sequences
387(37)
Roberto Barbui
Giulio Caravagna
Andrea Maggiolo-Schetini
Paolo Milazzo
Giovanni Pardini
Hybrid Systems and Biology: Continuous and Discrete Modeling for Systems Biology
424(25)
Luca Bortolussi
Alberto Policriti
π@ A π-Based Process Calculus for the Implementation of Compartmentalised Bio-inspired Calculi
449(58)
Cristian Versari
Roberto Gorrieri
A Gentle Introduction to Stochastic (Poly) Automata Collectives and the (Bio) Chemical Ground Form
507(18)
Gianluigi Zavattaro
Author Index 525