This book constitutes the refereed proceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2006, held in Trento, Italy, in October 2006. The 22 fully revised papers presented together with 2 invited talks were carefully reviewed and selected from 68 submissions. The papers present a variety of techniques from computer sciences, such as language design, concurrency theory, software engineering, and formal methods.

Modal Logics for Brane Calculus.- Deciding Behavioural Properties in Brane Calculi.- Probabilistic Model Checking of Complex Biological Pathways.- Type Inference in Systems Biology.- Stronger Computational Modelling of Signalling Pathways Using Both Continuous and Discrete-State Methods.- A Formal Approach to Molecular Docking.- Feedbacks and Oscillations in the Virtual Cell VICE.- Modelling Cellular Processes Using Membrane Systems with Peripheral and Integral Proteins.- Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets.- Regulatory Network Reconstruction Using Stochastic Logical Networks.- Identifying Submodules of Cellular Regulatory Networks.- Incorporating Time Delays into the Logical Analysis of Gene Regulatory Networks.- A Computational Model for Eukaryotic Directional Sensing.- Modeling Evolutionary Dynamics of HIV Infection.- Compositional Reachability Analysis of Genetic Networks.- Randomization and Feedback Properties of Directed Graphs Inspired by Gene Networks.- Computational Model of a Central Pattern Generator.- Rewriting Game Theory as a Foundation for State-Based Models of Gene Regulation.- Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast.- An In Silico Analogue of In Vitro Systems Used to Study Epithelial Cell Morphogenesis.- A Numerical Aggregation Algorithm for the Enzyme-Catalyzed Substrate Conversion.- Possibilistic Approach to Biclustering: An Application to Oligonucleotide Microarray Data Analysis.