This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, held in Rostock, Germany, in September 2008.
The 21 revised full papers presented together with the summaries of 5 invited papers were carefully reviewed and selected from more than 60 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): Hidde de Jong (auth.), Monika Heiner, Adelinde M. Uhrmacher (eds.)
Series: Lecture Notes in Computer Science 5307
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2008
Language: English
Pages: 403
Tags: Simulation and Modeling; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Software Engineering; Database Management; Computation by Abstract Devices
Front Matter....Pages -
Qualitative Modeling and Simulation of Bacterial Regulatory Networks....Pages 1-1
Integrated Analysis from Abstract Stochastic Process Algebra Models....Pages 2-4
An Exact Brownian Dynamics Method for Cell Simulation....Pages 5-6
Multiscale Modelling of Neuronal Signalling....Pages 7-7
Systems Biology of Halophilic Archaea....Pages 8-8
A Partial Granger Causality Approach to Explore Causal Networks Derived From Multi-parameter Data....Pages 9-27
Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe....Pages 28-43
Component-Based Modelling of RNA Structure Folding....Pages 44-62
A Language for Biochemical Systems....Pages 63-82
The Attributed Pi Calculus....Pages 83-102
The Continuous π -Calculus: A Process Algebra for Biochemical Modelling....Pages 103-122
Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems....Pages 123-140
Formal Analysis of Abnormal Excitation in Cardiac Tissue....Pages 141-155
The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock....Pages 156-175
SED-ML – An XML Format for the Implementation of the MIASE Guidelines....Pages 176-190
On Parallel Stochastic Simulation of Diffusive Systems....Pages 191-210
Large-Scale Design Space Exploration of SSA....Pages 211-230
Statistical Model Checking in BioLab : Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway....Pages 231-250
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology....Pages 251-268
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways....Pages 269-287
Compositional Definitions of Minimal Flows in Petri Nets....Pages 288-307
On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network....Pages 308-327
A Combinatorial Approach to Reconstruct Petri Nets from Experimental Data....Pages 328-346
An Exact Brownian Dynamics Method for Cell Simulation....Pages 347-366
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis....Pages 367-386
A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic Stem Cell Kinetics....Pages 387-401
Erratum: Analyzing a Discrete Model of Aplysia Central Pattern Generator....Pages E1-E1
Back Matter....Pages -
