References

  1. Accelera Organization, Inc. (2004): SystemVerilog 3.1a Language Reference Manual.
  2. R. Alur, T. Feder & T. A. Henzinger (1996): The benefits of relaxing punctuality. J ACM 43(1), pp. 116–146, doi:10.1145/227595.227602.
  3. R. Alur & T. A. Henzinger (1994): A really temporal logic. J ACM 41(1), pp. 181–203, doi:10.1145/174644.174651.
  4. P. Ballarini & M. L. Guerriero (2010): Query-based verification of qualitative trends and oscillations in biochemical systems. Theor. Comput. Sci. 411(20), pp. 2019–2036, doi:10.1016/j.tcs.2010.02.010.
  5. J. Barnat, L. Brim & D. Šafránek (2010): High-performance analysis of biological systems dynamics with the DiVin E model checker. Brief. in Bioinformatics 11, pp. 301–312, doi:10.1093/bib/bbp074.
  6. E. Bartocci, F. Corradini, E. Merelli & L. Tesei (2010): Detecting synchronisation of biological oscillators by model checking. Theoretical Computer Science 411(20), pp. 1999 – 2018, doi:10.1016/j.tcs.2009.12.019.
  7. G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page & D. Schneider (2005): Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response inıt Escherichia coli. In: ISMB (Supplement of Bioinformatics), pp. 19–28.
  8. M. de Berg, O. Cheong, M. van Kreveld & M. Overmars (2008): Computational Geometry: Algorithms and Applications, 3 edition. Springer, Berlin.
  9. L. Calzone, N. Chabrier-rivier, F. Fages & S. Soliman (2006): Machine learning biochemical networks from temporal logic properties. Trans Comput Syst Biol 4220, pp. 68–94, doi:10.1007/11880646_4.
  10. P. Dluhoš (2012): Specification and monitoring of oscillation properties in dynamical systems. Masaryk University. Available at http://is.muni.cz/th/269281/fi_m/thesis.pdf.
  11. A. Donzé & O. Maler (2010): Robust satisfaction of temporal logic over real-valued signals. In: FORMATS'10. Springer-Verlag, Berlin, Heidelberg, pp. 92–106, doi:10.1007/978-3-642-15297-9_9.
  12. A. Donzé, O. Maler, E. Bartocci, D. Nickovic, R. Grosu & S. Smolka (2012): On Temporal Logic and Signal Processing. Accepted to ATVA 2012..
  13. C. Eisner & D. Fisman (2008): Augmenting a regular expression-based temporal logic with local variables. In: FMCAD '08. IEEE Press, pp. 23:1–23:8, doi:10.1.1.140.3930.
  14. M. B. Elowitz & S. Leibler (2000): A synthetic oscillatory network of transcriptional regulators. Nature 403(6767), pp. 335–338, doi:10.1038/35002125.
  15. B. N. Kholodenko (2000): Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur J Biochem 267(6), pp. 1583–1588, doi:10.1046/j.1432-1327.2000.01197.x.
  16. M. Kvasnica, P. Grieder & M. Baoti\'c (2004): Multi-Parametric Toolbox (MPT).
  17. O. Maler & D. Nickovic (2004): Monitoring temporal properties of continuous signals. In: Proc. of FORMATS-FTRTFT. Springer, pp. 152–166, doi:10.1.1.102.2905.
  18. O. Maler, D. Nickovic & A. Pnueli (2008): Checking Temporal Properties of Discrete, Timed and Continuous Behaviors. In: Pillars of Computer Science, LNCS 4800. Springer, pp. 475–505, doi:10.1007/978-3-540-78127-1_26.
  19. R. Mateescu, P. T. Monteiro, E. Dumas & H. de Jong (2011): CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks. Theor. Comput. Sci. 412(26), pp. 2854–2883, doi:10.1016/j.tcs.2010.05.009.
  20. F. Miyoshi, Y. Nakayama, K. Kaizu, H. Iwasaki & M. Tomita (2007): A Mathematical Model for the Kai-Protein-Based Chemical Oscillator and Clock Gene Expression Rhythms in Cyanobacteria. Journal of Biological Rhythms 22(1), pp. 69–80, doi:10.1177/0748730406295749.
  21. D. Nickovic & O. Maler (2007): AMT: a property-based monitoring tool for analog systems. In: Proceedings of the 5th international conference on Formal modeling and analysis of timed systems, FORMATS'07. Springer-Verlag, Berlin, Heidelberg, pp. 304–319.
  22. A. Rizk, G. Batt, F. Fages & S. Soliman (2008): On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology. In: Proc. of CMSB'08. Springer, pp. 251–268, doi:10.1007/978-3-540-88562-7_19.
  23. J. Červený & L. Nedbal (2009): Metabolic Rhythms of the Cyanobacterium Cyanothece sp. ATCC 51142 Correlate with Modeled Dynamics of Circadian Clock. J Biol Rhythms 24(4), pp. 295–303, doi:10.1177/0748730409338367.

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