AbstractCell

Formal abstraction of quantitative semantics for protein-protein interaction cellular network models.

Publications

Static Analysis and Systems Biology Proceedings (SASB)

• Jérôme Feret & Andre Levchenko (Eds.). Proceedings of the 2nd International Workshop on Static Analysis and Systems Biology (SASB 2011). In Electronic Notes in Theoretical Computer Science, volume 284. © 2012, Elsevier Science.

• Jérôme Feret & Andre Levchenko (Eds.). Proceedings of the 1st International Workshop on Static Analysis and Systems Biology (SASB 2010). In Electronic Notes in Theoretical Computer Science, volume 272. © 2011, Elsevier Science.

Publications of the project

• Jérôme Feret. An algebraic approach for inferring and using symmetries in rule-based models. To appear in the PostProceedings of the 5th International Workshop on Static Analysis and Systems Biology (SASB 2014), in Electronic Notes in Theoretical Computer Science. © 2014, Elsevier Science.

• Norman Ferns,& Doina Precup. Bisimulation Metrics are Optimal Value Functions. In Proccedings of the 30th Conference on Uncertainty in Artificial Intelligence (UAI 2014), AUAI Press.

• Norman Ferns,& Sophia Knight,& Doina Precup. Bisimulation for Markov Decision Processes through Families of Functional Expressions. In , May 2014, Oxford, United Kingdom. Springer, Lecture Notes in Computer Science, 8464. © 2014, Springer.

• Jérôme Feret, Heinz Koeppl,& Tatjana Petrov. Stochastic fragments: A framework for the exact reduction of the stochastic semantics of rule-based models. In International Journal of Software and Informatics, volume 7(4). © 2013, ISCAS.

• Ferdinanda Camporesi, Jérôme Feret,& Jonathan Hayman. Context-sensitive flow analyses: a hierarchy of model reductions. In Proceedings of the 11th Conference on Computational Methods in Systems Biology (CMSB 2013), in Lecture Note in BioInformatics, number 8130. © 2013, Springer.

• Jérôme Feret, Thomas Henzinger, Heinz Koeppl,& Tatjana Petrov. Lumpability Abstractions of Rule-based Systems. In Theoretical Computer Science, special issue on MeCBIC 2009-2010, G. Ciobanu & M. Koutny (Ed.). © 2012, Elsevier Science.

• Tatjana Petrov, Jérôme Feret,& Heinz Koeppl. Reconstructing species-based dynamics from reduced stochastic rule-based models. In Proceedings of the Winter Simulation Conference (WSC 2012).

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh,& Glynn Winskel. Rewriting and Pathway Reconstruction for Rule-Based Models. In Proceedings of the 32nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012), in Leibniz International Proceedings in Informatics, volume 18, pp 276--288. © 2012, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.

• Jonathan Hayman, Tobias Heindel. Pattern Graphs and Rule-Based Models: the semantics of Kappa. In Proceedings of the 16th International Conference on Foundations of Software Science and Computation Structures (FOSSACS'13), in Lecture Notes in Computer Science. © 2013, Springer. To appear.

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

• Jérôme Feret. Formal model reduction. In Static Analysis Symposium (SAS 2011), number 6887 in Lecture Notes in Computer Science, p 6. © 2011, Springer.

• Ferdinanda Camporesi, Jérôme Feret, Heinz Koeppl,& Tatjana Petrov.
  Combining model reductions. In Mathematical Foundations of Programming Semantics (MFPS XXVI), in Electronnic Notes in Theoretical Computer Science, volume 265, pp 73--96. © 2010, Elsevier Science.

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

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harlmer,& 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, 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.

• 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.