Master AIV

UE: Computational Biology II

Russ' website

Static analysis of protein-protein interactions networks

December 19th 2012

Slides

• Introduction
• Reachability Analysis of Rule-based Models
• Some notions of information flow
• Formal model reduction of ODE semantics
• Model reduction of stochastic rules-based models


• All in one

Suggested references

• 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.

• Ferdinanda Camporesi, Jérôme Feret. Formal reduction of rule-based models. In Mathematical Foundations of Programming Semantics (MFPS XXVII), in Electronic Notes in Theoretical Computer Science, volume 276, pp 31--61. © 2011, Elsevier Science.

• Jérôme Feret. Fragments-based model reduction: some case studies. In Interactions between Computer Science and Biology (CS2Bio 2010), in Electronic Notes in Theoretical Computer Science, volume 268, pp 77--96 © 2010, Elsevier Science.

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Jérôme Feret, Last modified: 21 Dec 2012, 09:12:56 CET