Abstract interpreation of protein-protein interactions networks
These lectures have been given at ENS Lyon, during a winter school on rule-based modelling.
- Practical works
- Question sets
The following (free) software are required to do the practical works.
- Jérôme Feret.
Reachability analysis of biological signalling pathways by abstract interpretation.
In International Conference of Computational Methods in Sciences and Engineering(ICCMSE'07),
numero 963(2) in American Institute of Physics conference proceedings.
2007, © American Institute of Physics.
- Vincent Danos, Jérôme Feret, Walter Fontana,& Jean Krivine.
Abstract interpretation of cellular signalling networks.
In Verification, Model Checking, and Abstract Interpretation(VMCAI 2008),
number 4905 in Lecture Notes in Computer Sciences.
2008, © Springer.
- Jérôme Feret, Vincent Danos, Jean Krivine, Russell Harmer,& Walter Fontana.
Internal coarse-graining of molecular systems.
Proceedings of National Academy of Sciences of the United States of America(PNAS), volume 106.(16). 2009, © National Academy of Sciences.
- Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine. Abstracting the differential semantics of rule-based models: exact and automated model reduction . In Logic in Computer Science (LICS 2010). 2010, © IEEE Computer Society.
- Jérôme Feret, Thomas Henzinger, Heinz Koeppl,& Tatjana Petrov. Lumpability Abstractions of Rule-based Systems. In The 4th Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 2010), to appear in Electronic Proceedings in Theoretical Computer Science. © 2010, Elsevier Science.
- Ferdinanda Camporesi, Jérôme Feret, Heinz Koeppl,& Tatjana Petrov. Automatic reduction of stochastic rules-based models in a nutshell. In International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2010), numero 1281(2) in American Institute of Physics conference proceedings. 2010, © American Institute of Physics.
- Russell Harmer, Vincent Danos, Jérôme Feret, Jean Krivine,& Walter Fontana. Intrinsic Information Carriers in Combinatorial Dynamics Systems. In Chaos, volume 20(3), 2010, © American Institute of Physics.
- Ferdinanda Camporesi, Jérôme Feret, Heinz Koeppl,& Tatjana Petrov. Combining model reductions. In Mathematical Foundations of Programming Semantics (MFPS XXVI), to appear in Electronnic Notes in Theoretical Computer Science, volume 265, pp 73--96. © 2010, Elsevier Science.