Computational Methods in Systems Biology: 6th International Conference CMSB 2008, Rostock, Germany, October 12-15, 2008. Proceedings

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Springer Science & Business Media, 07.10.2008 - 403 Seiten
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This volume contains the proceedings of the 6th Conference on Computational Methods in Systems Biology (CMSB) held in October 2008 in Rostock/ Warnemunde. ¨ The CMSB conference series was established in 2003 to promote the c- vergence of (1) modelers, physicists, mathematicians, and theoretical computer scientists from ?elds such as language design, concurrency theory, software ve- ?cation, and (2) molecular biologists, physicians, neuroscientists joined by their interest in a systems-level understanding of cellular physiology and pathology. Sincethistime,theconferencehastakenplaceannually. Theconferencehasbeen held in Italy, France, and the UK, and we were glad to host CMSB in Germany for the ?rst time. The summaries of the invited talks by Hidde de Jong, Jane Hillston, Koichi Takahashi, Nicolas Le Novere, and Dieter Oesterhelt are included at the - ginning of the proceedings. The 21 regular 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 ?ux analysis, and case studies. They were - lected out of more than 60 submissions by a careful reviewing process. Each paper received at least three reviews from members of the Program Committee consistingof27renownedscientistsfromsevencountries. We wouldliketothank all members of the Program Committee and the referees for the thorough and insightful reviews and the constructive discussions. Due to the number of hi- quality submissions, the decision on which papers to accept or reject was not easy. Therefore, we integrated a rebuttal phase for the ?rst time.
 

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Inhalt

Qualitative Modeling and Simulation of Bacterial Regulatory
1
Joachim Niehren INRIA Futurs Lille France
5
Multiscale Modelling of Neuronal Signalling
7
Functional Evolution of RibozymeCatalyzed Metabolisms in
28
ComponentBased Modelling of RNA Structure Folding
44
A Language for Biochemical Systems
63
The Attributed Pi Calculus
83
A Process Algebra for Biochemical
103
LargeScale Design Space Exploration of SSA
211
Applications to the Automated
231
On a Continuous Degree of Satisfaction of Temporal Logic Formulae
251
A Model Checking Approach to the Parameter Estimation
269
Compositional Definitions of Minimal Flows in Petri Nets
288
On Inner and Outer Descriptions of the SteadyState Flux Cone of
308
A Combinatorial Approach to Reconstruct Petri Nets from
328
Analyzing a Discrete Model of Aplysia Central Pattern Generator
347

Automatic Complexity Analysis and Model Reduction of Nonlinear
123
Formal Analysis of Abnormal Excitation in Cardiac Tissue
141
The Distribution of Mutational Effects on Fitness in a Simple Circadian
156
SEDML An XML Format for the Implementation of the MIASE
176
Nicolas Le Novere European Bioinformatics Institute UK
191
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis
367
A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic
387
Author Index
403
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