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.
Author(s): Lisa Bartoli, Pier Luigi Martelli, Ivan Rossi (auth.), Pierpaolo Degano, Roberto Gorrieri (eds.)
Series: Lecture Notes in Computer Science 5688 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2009
Language: English
Pages: 329
Tags: Computational Biology/Bioinformatics; Simulation and Modeling; Computation by Abstract Devices; Numeric Computing; Cell Biology; Computer Appl. in Life Sciences
Front Matter....Pages -
Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks....Pages 1-17
The Equivalence between Biology and Computation....Pages 18-25
BlenX4Bio – BlenX for Biologists....Pages 26-51
Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network....Pages 52-67
Quantitative Pathway Logic for Computational Biology....Pages 68-82
A Prize-Collecting Steiner Tree Approach for Transduction Network Inference....Pages 83-95
Formal Analysis of the Genetic Toggle....Pages 96-110
Control Strategies for the Regulation of the Eukaryotic Heat Shock Response....Pages 111-125
Computing Reachable States for Nonlinear Biological Models....Pages 126-141
On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle....Pages 142-157
The κ -Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages....Pages 158-172
Approximation of Event Probabilities in Noisy Cellular Processes....Pages 173-188
Equivalence and Discretisation in Bio-PEPA....Pages 189-204
Improved Parameter Estimation for Completely Observed Ordinary Differential Equations with Application to Biological Systems....Pages 205-217
A Bayesian Approach to Model Checking Biological Systems....Pages 218-234
Dynamic Compartments in the Imperative π -Calculus....Pages 235-250
Probabilistic Approximations of Signaling Pathway Dynamics....Pages 251-265
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties....Pages 266-280
On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process....Pages 281-295
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams....Pages 296-312
Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models....Pages 313-327
Back Matter....Pages -
