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This volume, the 7th in the Transactions on Computational Systems Biology series, contains a fully refereed and carefully selected set of papers from two workshops: BioConcur 2004 held in London, UK in August 2004 and BioConcur 2005 held in San Francisco, CA, USA in August 2005.
The 8 papers chosen for this special issue are devoted to various aspects of computational methods, algorithms, and techniques in bioinformatics such as modeling of signaling pathways, gene regulation in pi-calculus, relations between regulator graphs and Petri nets, translation of SBML models to stochastic pi-calculus, use of graph theory to model biological networks, distributed model checking with biochemical Kripke structures, graphical notation for stochastic pi-calculus, as well as differentiation and homeostatic behavior of boolean dynamic systems.
The Transactions on Computational Systems Biology series is devoted to inter- and multidisciplinary research in computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomen
Content Level »Research
Keywords »Algorithms - algorithm - bioinformatics - biology - life sciences - model checking - modeling - petri net
Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA.- Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch.- From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits.- Translating SBML Models into the Stochastic ?-Calculus for Stochastic Simulation.- Graph Theory for Rule-Based Modeling of Biochemical Networks.- Adapting Biochemical Kripke Structures for Distributed Model Checking.- A Graphical Representation for Biological Processes in the Stochastic pi-Calculus.- On Differentiation and Homeostatic Behaviours of Boolean Dynamical Systems.- A Specification Language and a Framework for the Execution of Composite Models in Systems Biology.- A Specification Language and a Framework for the Execution of Composite Models in Systems Biology.