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.

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.