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 revised full papers presented together with 2 invited talks were carefully reviewed and selected from 68 submissions. The papers present a variety of techniques from computer science, such as language design, concurrency theory, software engineering, and formal methods, for biologists, physicists, and mathematicians interested in the systems-level understanding of cellular processes.
Author(s): Marino Miculan, Giorgio Bacci (auth.), Corrado Priami (eds.)
Series: Lecture Notes in Computer Science 4210
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2006
Language: English
Pages: 323
Tags: Simulation and Modeling; Bioinformatics; Computer Appl. in Life Sciences; Software Engineering; Database Management; Computation by Abstract Devices
Front Matter....Pages -
Modal Logics for Brane Calculus....Pages 1-16
Deciding Behavioural Properties in Brane Calculi....Pages 17-31
Probabilistic Model Checking of Complex Biological Pathways....Pages 32-47
Type Inference in Systems Biology....Pages 48-62
Stronger Computational Modelling of Signalling Pathways Using Both Continuous and Discrete-State Methods....Pages 63-77
A Formal Approach to Molecular Docking....Pages 78-92
Feedbacks and Oscillations in the Virtual Cell VICE....Pages 93-107
Modelling Cellular Processes Using Membrane Systems with Peripheral and Integral Proteins....Pages 108-126
Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets....Pages 127-141
Regulatory Network Reconstruction Using Stochastic Logical Networks....Pages 142-154
Identifying Submodules of Cellular Regulatory Networks....Pages 155-168
Incorporating Time Delays into the Logical Analysis of Gene Regulatory Networks....Pages 169-183
A Computational Model for Eukaryotic Directional Sensing....Pages 184-195
Modeling Evolutionary Dynamics of HIV Infection....Pages 196-211
Compositional Reachability Analysis of Genetic Networks....Pages 212-226
Randomization and Feedback Properties of Directed Graphs Inspired by Gene Networks....Pages 227-241
Computational Model of a Central Pattern Generator....Pages 242-256
Rewriting Game Theory as a Foundation for State-Based Models of Gene Regulation....Pages 257-270
Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast....Pages 271-284
An In Silico Analogue of In Vitro Systems Used to Study Epithelial Cell Morphogenesis....Pages 285-297
A Numerical Aggregation Algorithm for the Enzyme-Catalyzed Substrate Conversion....Pages 298-311
Possibilistic Approach to Biclustering: An Application to Oligonucleotide Microarray Data Analysis....Pages 312-322
Back Matter....Pages -
