A calculus of mobile processes, II
Information and Computation
A compositional approach to performance modelling
A compositional approach to performance modelling
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Information Processing Letters
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Quantitative analysis of biochemical signalling pathways
Proceedings of the 2nd international conference on Performance evaluation methodologies and tools
International Journal of Data Mining and Bioinformatics
Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
Relating continuous and discrete PEPA models of signalling pathways
Theoretical Computer Science
From Gene Regulation to Stochastic Fusion
UC '08 Proceedings of the 7th international conference on Unconventional Computing
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Modeling of Genetic Regulatory Network in Stochastic π-Calculus
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
Rule-based programming for integrative biological modeling
Natural Computing: an international journal
A stochastic pi calculus for concurrent objects
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Hierarchical modeling for computational biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Process algebras in systems biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Computational thinking in biology
Transactions on computational systems biology VIII
Structural analysis for stochastic process algebra models
AMAST'10 Proceedings of the 13th international conference on Algebraic methodology and software technology
Refining dynamics of gene regulatory networks in a stochastic π-calculus framework
Transactions on computational systems biology XIII
A compositional approach to the stochastic dynamics of gene networks
Transactions on Computational Systems Biology IV
The attributed pi-calculus with priorities
Transactions on Computational Systems Biology XII
A compositional approach for modeling and simulation of bio-molecular systems
Proceedings of the Winter Simulation Conference
General patterns of interaction in stochastic fusion
Natural Computing: an international journal
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We propose to model the dynamics of gene regulatory networks as concurrent processes in the stochastic pi calculus. As a first case study, we show how to express the control of transcription initiation at the lambda switch, a prototypical example where cooperative enhancement is crucial. This requires concurrent programming techniques that are new to systems biology, and necessitates stochastic parameters that we derive from the literature. We test all components of our model by exhaustive stochastic simulations. A comparison with previous results reported in the literature, experimental and simulation based, confirms the appropriateness of our modeling approach.