Source: http://www.ens-lyon.fr/DI/er-05-tba/?lang=en
Timestamp: 2019-04-19 04:59:11+00:00

Document:
The goal of this course is to give an overview on rule-based modelling.
modeling/programming of combinatorial molecular networks.
with an interest in biomodelling.
Pedagogical materials will be in English.
Lectures will be given in English.
Basics of modeling : Petri-Nets, mass action law, detection of equilibriums and steady states, thermodynamic limit (Kurz theorem).
Introduction to kappa : Notion of model in biology, syntax and operational semantics.
Dynamics : Gillespie’s algorithm, scalability issue, causality.
Static analysis : Qualitative analysis, reachability (completeness result), species enumeration algorithm.
Model reduction : Information flow, ODE semantics, stochastic semantics.
Energy and syntax : Information flow, ODE semantics, stochastic semantics.
Extensions : Compartments, agent variants,diffusion.
This course requires no prelimary knowledge.
The fundamental notions which will be used in this course will be properly introduced.
V. Danos, C. Laneve. Formal Molecular Biology. In Theoretical Computer Science 325, 2004.
V. Danos, J. Feret, W. Fontana, R. Harmer,& J. Krivine. Rule-based modelling of cellular signalling. Invited in International Conference on Concurrency Theory(CONCUR 2007), number 4703 in Lecture Notes in Computer Science. 2007, © Springer.
J. Krivine, V. Danos, A. Benecke. Modelling epigenetic information maintenance: a Kappa tutorial Invited tutorial in Computer Aided Verification(CAV 2009), number 5643 in Lectures Notes in Computer Science. 2009, © Springer.
V. Danos, J. Feret, W. Fontana,& J. Krivine. Scalable modelling of biological pathways. Invited in Asian Symposium on Programming Systems(APLAS 2007), number 4807 in Lecture Notes in Computer Science. 2007, © Springer.
V. Danos, J. Feret, W. Fontana, R. Harmer,& Jean Krivine. Abstracting the differential semantics of rule-based models: exact and automated model reduction. Invited in Logic in Computer Science (LICS 2010). 2010, © IEEE Computer Society.
V. Danos, N. Oury. Energy and Termination. In Developments in Computational Models 2010, Causality, Computation, and Physics (DCM 2010). 2010, © Electronic Proceedings in Theoretical Computer Science.

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