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.

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.