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Computational Methods in Systems Biology 6th International Conference CMSB 2008, Rostock, Germany, October 12-15, 2008. Proceedings
This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, held in...
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The Attributed Pi Calculus
The attributed pi calculus $({\phi({\mathcal L})})$ forms an...
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The Continuous π-Calculus: A Process Algebra for Biochemical Modelling
We introduce the continuous π -calculus, a process algebra for modelling behaviour and variation in molecular systems. Key features of...
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The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock
The distribution of mutational effects on fitness (DME F ) is of fundamental importance for many questions in biology....
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Stochastic Analysis of Amino Acid Substitution in Protein Synthesis
We present a formal analysis of amino acid replacement during mRNA translation. Building on an abstract stochastic model of arrival of tRNAs and...
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On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network
Constraint-based approaches have proved successful in analyzing complex metabolic networks. They restrict the range of all possible behaviors that a...
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Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe
The origin and evolution of metabolism is an interesting field of research with many unsolved questions. Simulation approaches, even though mostly...
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Formal Analysis of Abnormal Excitation in Cardiac Tissue
We present the Piecewise Linear Approximation Model of Ion Channel contribution (PLAMIC) to cardiac excitation. We use the PLAMIC model to conduct...
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A Combinatorial Approach to Reconstruct Petri Nets from Experimental Data
For many aspects of health and disease, it is important to understand different phenomena in biology and medicine. To gain the required insight,...
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Multiscale Modelling of Neuronal Signalling
Transduction and transmission of an input signal by a neuronal dendrite involves generation, integration and propagation of at least four kinds of...
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Erratum: Analyzing a Discrete Model of Aplysia Central Pattern Generator
We present a discrete formal model of the central pattern generator (CPG) located in the buccal ganglia of Aplysia that is responsible for mediating...
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Systems Biology of Halophilic Archaea
Systems biology is spread over all branches of life science and attracts biologists, mathematicians, physicists, computer scientists, and engineers...
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A Partial Granger Causality Approach to Explore Causal Networks Derived From Multi-parameter Data
Background: Inference and understanding of gene networks from experimental data is an important but complex problem in molecular biology. Map** of...
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SED-ML – An XML Format for the Implementation of the MIASE Guidelines
Share and reuse of biochemical models have become two of the main issues in the field of Computational Systems Biology. There already exist...
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A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic Stem Cell Kinetics
The therapeutic potential of stem cells due to their ability to build and maintain tissues and organs is widely recognised. Much can be learned by...
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An Exact Brownian Dynamics Method for Cell Simulation
As we obtain better abilities to observe cellular biochemistry at the single cell / molecular levels, such as through fluorescent correlation...
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Qualitative Modeling and Simulation of Bacterial Regulatory Networks
The adaptation of microorganisms to their environment is controlled at the molecular level by large and complex networks of biochemical reactions...
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A Model Checking Approach to the Parameter Estimation of Biochemical Pathways
Model checking has historically been an important tool to verify models of a wide variety of systems. Typically a model has to exhibit certain...
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On Parallel Stochastic Simulation of Diffusive Systems
The parallel simulation of biochemical reactions is a very interesting problem: biochemical systems are inherently parallel, yet the majority of the...
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On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology
Finding mathematical models satisfying a specification built from the formalization of biological experiments, is a common task of the modeller that...