1. Maximino Aldana & Philippe Cluzel (2003): A natural class of robust networks. Proceedings of the National Academy of Sciences 100(15), pp. 8710–8714, doi:10.1073/pnas.1536783100.
  2. Rajeev Alur & David L. Dill (1994): A Theory of Timed Automata. Theor. Comput. Sci. 126(2), pp. 183–235, doi:10.1016/0304-3975(94)90010-8.
  3. Étienne André, Thomas Chatain, Laurent Fribourg & Emmanuelle Encrenaz (2008): An Inverse Method for Parametric Timed Automata. Electronic Notes in Theoretical Computer Science 223(0), pp. 29 – 46, doi:10.1016/j.entcs.2008.12.029.
  4. Étienne André (2010): IMITATOR II: A Tool for Solving the Good Parameters Problem in Timed Automata. In: INFINITY, pp. 91–99, doi:10.4204/EPTCS.39.7.
  5. Patricia Bouyer, Nicolas Markey & Pierre-Alain Reynier (2006): Robust Model-Checking of Linear-Time Properties in Timed Automata. In: LATIN, pp. 238–249, doi:10.1007/11682462_25.
  6. Nathalie Chabrier-Rivier, François Fages & Sylvain Soliman (2005): The Biochemical Abstract Machine BIOCHAM. In: Vincent Danos & Vincent Schachter: Computational Methods in Systems Biology, Lecture Notes in Computer Science 3082. Springer Berlin Heidelberg, pp. 172–191, doi:10.1007/978-3-540-25974-9_14.
  7. Claudine Chaouiya, Elisabeth Remy, Brigitte Mossé & Denis Thieffry (2003): Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. In: Luca Benvenuti, Alberto De Santis & Lorenzo Farina: Positive Systems, Lecture Notes in Control and Information Sciences 294. Springer, Berlin / Heidelberg, pp. 830–832, doi:10.1007/978-3-540-44928-7_17.
  8. Federica Ciocchetta, Adam Duguid, Stephen Gilmore, Maria Luisa Guerriero & Jane Hillston (2009): The Bio-PEPA Tool Suite. International Conference on Quantitative Evaluation of Systems, pp. 309–310, doi:10.1109/QEST.2009.27.
  9. Conrado Daws & Piotr Kordy (2006): Symbolic Robustness Analysis of Timed Automata. In: FORMATS, pp. 143–155, doi:10.1007/11867340_11.
  10. Lorenzo Dematté, Corrado Priami & Alessandro Romanel (2008): Modelling and simulation of biological processes in BlenX. SIGMETRICS Perform. Eval. Rev. 35, pp. 32–39, doi:10.1145/1364644.1364653.
  11. Alexandre Donzé (2010): Breach, a Toolbox for Verification and Parameter Synthesis of Hybrid Systems. In: Proceedings of the 22Nd International Conference on Computer Aided Verification, CAV'10. Springer-Verlag, Berlin, Heidelberg, pp. 167–170, doi:10.1007/978-3-642-14295-6_17.
  12. Jasmin Fisher & Thomas A. Henzinger (2007): Executable cell biology.. Nature Biotechnology 25(11), pp. 1239–1249, doi:10.1038/nbt1356.
  13. Laurent Fribourg & Ulrich Kühne (2011): Parametric Verification and Test Coverage for Hybrid Automata Using the Inverse Method. In: Giorgio Delzanno & Igor Potapov: Reachability Problems, LNCS 6945. Springer Berlin Heidelberg, pp. 191–204, doi:10.1007/978-3-642-24288-5_17.
  14. Rajat P. Garg & Ilya Sharapov (2002): Techniques for Optimizing Applications: High Performance Computing. Prentice Hall Professional Technical Reference.
  15. Thomas Hune, Judi Romijn, Mariëlle Stoelinga & Frits Vaandrager (2002): Linear parametric model checking of timed automata. The Journal of Logic and Algebraic Programming 52-53(0), pp. 183 – 220, doi:10.1016/S1567-8326(02)00037-1.
  16. Hidde de Jong, Johannes Geiselmann, Céline Hernandez & Michel Page (2003): Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 19(3), pp. 336–344, doi:10.1093/bioinformatics/btf851.
  17. Sarah Killcoyne, Gregory W. Carter, Jennifer Smith & John Boyle (2009): Cytoscape: a community-based framework for network modeling.. Methods in molecular biology (Clifton, N.J.) 563, pp. 219–239, doi:10.1007/978-1-60761-175-2_12.
  18. P. T. Kordy, R. Langerak & J. W. Polderman (2010): Re-verification of a Lip Synchronization Protocol using Robust Reachability. Electronic Proceedings in Theoretical Computer Science 20, pp. 49–62, doi:10.4204/EPTCS.20.5.
  19. Paola Lecca, Alida Palmisano, Adaoha Ihekwaba & Corrado Priami (2010): Calibration of dynamic models of biological systems with KInfer. European Biophysics Journal 39(6), pp. 1019 – 1039, doi:10.1007/s00249-009-0520-3.
  20. Petros Lenas, Malcolm Moos Jr. & Frank P. Luyten (2009): Developmental Engineering: A New Paradigm for the Design and Manufacturing of Cell-Based Products. Part II. From Genes to Networks: Tissue Engineering from the Viewpoint of Systems Biology and Network Science. Tissue Engineering Part B: Reviews 15(4), pp. 395–422, doi:10.1089/ten.teb.2009.0461.
  21. Wenhui Liao & Qiang Ji (2009): Learning Bayesian network parameters under incomplete data with domain knowledge. Pattern Recognition 42(11), pp. 3046 – 3056, doi:10.1016/j.patcog.2009.04.006.
  22. Pedro Mendes, Stefan Hoops, Sven Sahle, Ralph Gauges, Joseph Dada & Ursula Kummer (2009): Computational modeling of biochemical networks using COPASI systems biology. In: Ivan V. Maly, John M. Walker & John M. Walker: Systems Biology, chapter 2, Methods in Molecular Biology 500. Humana Press, Totowa, NJ, pp. 17–59, doi:10.1007/978-1-59745-525-1_2.
  23. Joseph S. Miller (2000): Decidability and Complexity Results for Timed Automata and Semi-linear Hybrid Automata. In: Proceedings of the Third International Workshop on Hybrid Systems: Computation and Control, HSCC '00. Springer-Verlag, London, UK, pp. 296–309, doi:10.1007/3-540-46430-1_26.
  24. Masao Nagasaki, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda & Satoru Miyano (2011): Cell illustrator 4.0: a computational platform for systems biology.. Stud Health Technol Inform 162, pp. 160–81.
  25. Corrado Priami (2009): Algorithmic systems biology. Commun. ACM 52, pp. 80–88, doi:10.1145/1506409.1506427.
  26. Stefano Schivo, Jetse Scholma, Brend Wanders, Ricardo A. Urquidi Camacho, Paul E. van der Vet, Marcel Karperien, Rom Langerak, Jaco van de Pol & Janine N. Post (2013): Modelling biological pathway dynamics with Timed Automata. IEEE Journal of Biomedical and Health Informatics In press, doi:10.1109/JBHI.2013.2292880.
  27. Jetse Scholma, Stefano Schivo, Ricardo A. Urquidi Camacho, Jaco van de Pol, Marcel Karperien & Janine N. Post (2014): Biological networks 101: Computational modeling for molecular biologists. Gene 533(1), pp. 379–384, doi:10.1016/j.gene.2013.10.010.
  28. Adam Smith, Wen Xu, Yao Sun, James Faeder & G Elisabeta Marai (2012): RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. BMC Bioinformatics 13(Suppl 8), pp. S3, doi:10.1186/1471-2105-13-S8-S3.
  29. Jan Tretmans (2011): Model-Based Testing and Some Steps towards Test-Based Modelling. In: Marco Bernardo & Valérie Issarny: Formal Methods for Eternal Networked Software Systems, Lecture Notes in Computer Science 6659. Springer, Berlin / Heidelberg, pp. 297–326, doi:10.1007/978-3-642-21455-4_9.
  30. Martin Wulf, Laurent Doyen, Nicolas Markey & Jean-François Raskin (2008): Robust safety of timed automata. Form. Methods Syst. Des. 33(1-3), pp. 45–84, doi:10.1007/s10703-008-0056-7.

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