Formal Methods for Computational Systems Biology

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.

Inhalt
Regular Lectures.- Sensitivity Analysis of Stochastic Models of Bistable Biochemical Reactions.- Pathway Logic.- 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.- The BlenX Language: A Tutorial.- BISCA Talks.- Cells in Silico: A Holistic Approach.- The Calculus of Looping Sequences.- Hybrid Systems and Biology.- ?@: A ?-Based Process Calculus for the Implementation of Compartmentalised Bio-inspired Calculi.- A Gentle Introduction to Stochastic (Poly)Automata Collectives and the (Bio)Chemical Ground Form.