Information Processing Letters
Cell Cycle Control in Eukaryotes: A BioSpi model
Electronic Notes in Theoretical Computer Science (ENTCS)
Theoretical Computer Science
A Process Model of Actin Polymerisation
Electronic Notes in Theoretical Computer Science (ENTCS)
Efficient, correct simulation of biological processes in the stochastic pi-calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
A compositional approach to the stochastic dynamics of gene networks
Transactions on Computational Systems Biology IV
A graphical representation for biological processes in the stochastic pi-calculus
Transactions on Computational Systems Biology VII
On the use of temporal formal logic to model gene regulatory networks
CIBB'09 Proceedings of the 6th international conference on Computational intelligence methods for bioinformatics and biostatistics
BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
Electronic Notes in Theoretical Computer Science (ENTCS)
Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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Rho GTP-binding proteins play a key role as molecular switches in many cellular activities. In response to extracellular stimuli and with the help of regulators (GEF, GAP, Effector, GDI), these proteins serve as switches that interact with their environment in a complex manner. Based on the structure of a published ordinary differential equations (ODE) model, we first present a generic process model for the Rho GTP-binding proteins, and compare it with the ODE model. We then extend the basic model to include the behaviour of the GDI regulators and explore the parameter space for the extended model with respect to biological data from the literature. We discuss the challenges this extension brings and the directions of further research. In particular, we present techniques for modular representation and refinement of process models, where, for example, different Rho proteins with different rates for regulator interactions can be given as instances of the same parametric model.