A calculus of mobile processes, II
Information and Computation
Information Processing Letters
Biocomputation: modeling and analyzing biomolecular networks
Computing in Science and Engineering
Time Petri Nets for Modelling and Analysis of Biochemical Networks
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
Semantics of Biological Regulatory Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Model Checking Probabilistic and Stochastic Extensions of the π-Calculus
IEEE Transactions on Software Engineering
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
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
Petri nets for systems and synthetic 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
Incorporating time delays into the logical analysis of gene regulatory networks
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
A compositional approach to the stochastic dynamics of gene networks
Transactions on Computational Systems Biology IV
Gene regulation in the pi calculus: simulating cooperativity at the lambda switch
Transactions on Computational Systems Biology VII
PRISM: a tool for automatic verification of probabilistic systems
TACAS'06 Proceedings of the 12th international conference on Tools and Algorithms for the Construction and Analysis of Systems
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Abstract Interpretation of Dynamics of Biological Regulatory Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Concretizing the process hitting into biological regulatory networks
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Under-Approximating cut sets for reachability in large scale automata networks
CAV'13 Proceedings of the 25th international conference on Computer Aided Verification
Under-approximation of Reachability in Multivalued Asynchronous Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
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In this paper, we introduce a framework allowing to model and analyse efficiently Gene Regulatory Networks (GRNs) in their temporal and stochastic aspects. The analysis of stable states and inference of René Thomas' discrete parameters derives from this logical formalism. We offer a compositional approach which comes with a natural translation to the Stochastic π-Calculus. The method we propose consists in successive refinements of generalised dynamics of GRNs. We illustrate the merits and scalability of our framework on the control of the differentiation in a GRN generalising metazoan segmentation processes, and on the analysis of stable states within a large GRN studied in the scope of breast cancer researches.