Computational Methods in Systems Biology

This volume contains the proceedings of the 7th Conference on Computational Methods in Systems Biology (CMSB 2009), held in Bologna, from August 31 to September 1, 2009. The ?rst CMSB was held in Trento in 2003, bringing together life scientists, computer scientists, engineers and physicists. The goal was to promote the c- vergence of di?erent disciplines aiming at a new understanding and description of biological systems, ?rmly ground in formal models, supported by compu- tionallanguagesandtools,ando?eringnew methodsofanalysis.The conference then moved to Paris in 2004, Edinburgh in 2005, Trento in 2006, Edinburgh in 2007 and Rostock/Warnemunde ¨ in 2008. This year the conference attracted about 45 submissions form 18 countries, mainly from Europe and North America, but also from Asia and Australia. We wish to thank all authors for their interest in CMSB 2009. After careful disc- sions, the Programme Committee eventually selected 18 papers for presentation at the conference. Each of them was accurately refereed by at least three - viewers, who delivered detailed and insightful comments and suggestions. The Conference Chairmen warmly thank all the members of the Programme C- mittee and all their sub-referees for the excellent support they gave, as well as for the friendly and constructive discussions. We also would like to thank the authorsfor havingrevisedtheir papers to addressthe comments andsuggestions by the referees.

Klappentext

This book constitutes the refereed proceedings of the 7th International Conference on Computational Methods in Systems Biology, CMSB 2009, held in Bologna, Italy, August 31 - September 1, 2009.

The 18 revised full papers presented together with the summaries of 3 invited papers were carefully reviewed and selected from more than 45 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.

Inhalt
Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks.- The Equivalence between Biology and Computation.- BlenX4Bio BlenX for Biologists.- Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network.- Quantitative Pathway Logic for Computational Biology.- A Prize-Collecting Steiner Tree Approach for Transduction Network Inference.- Formal Analysis of the Genetic Toggle.- Control Strategies for the Regulation of the Eukaryotic Heat Shock Response.- Computing Reachable States for Nonlinear Biological Models.- On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle.- The ?-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages.- Approximation of Event Probabilities in Noisy Cellular Processes.- Equivalence and Discretisation in Bio-PEPA.- Improved Parameter Estimation for Completely Observed Ordinary Differential Equations with Application to Biological Systems.- A Bayesian Approach to Model Checking Biological Systems.- Dynamic Compartments in the Imperative ?-Calculus.- Probabilistic Approximations of Signaling Pathway Dynamics.- A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties.- On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process.- CSL Model Checking of Biochemical Networks with Interval Decision Diagrams.- Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models.