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: advanced lectures

This book presents a set of 14 papers accompanying the lectures of leading researchers given at the 8th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008, held in Bertinoro, Italy in June 2008. SFM 2008 was devoted to formal techniques for computational systems biology and covered several aspects of the field, including computational models, calculi and logics for biological systems, and verification and simulation methods. The first part of this volume comprises nine papers based on regular lectures, the second part of this volume comprises five papers based on talks given by people involved in the Italian BISCA research project on Bio-Inspired Systems and Calculi with Applications. Front Matter....Pages - Sensitivity Analysis of Stochastic Models of Bistable Biochemical Reactions....Pages 1-20 Pathway Logic....Pages 21-53 Formal Cell Biology in Biocham....Pages 54-80 Hierarchical Modeling for Computational Biology....Pages 81-124 Simulation Methods in Systems Biology....Pages 125-167 Membrane Computing as a Modeling Framework. Cellular Systems Case Studies....Pages 168-214 Petri Nets for Systems and Synthetic Biology....Pages 215-264 Process Algebras in Systems Biology....Pages 265-312 The BlenX Language: A Tutorial....Pages 313-365 Cells in Silico : A Holistic Approach....Pages 366-386 The Calculus of Looping Sequences....Pages 387-423 Hybrid Systems and Biology....Pages 424-448 π @: A π -Based Process Calculus for the Implementation of Compartmentalised Bio-inspired Calculi....Pages 449-506 A Gentle Introduction to Stochastic (Poly)Automata Collectives and the (Bio)Chemical Ground Form....Pages 507-523 Back Matter....Pages -