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Barbaric Robustness Monitoring Revisited for STL* in Parasim

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Computational Methods in Systems Biology (CMSB 2019)

Abstract

In our previous work, we have introduced an extension of signal temporal logic called STL* that allows expressing freezing of values referred within temporal operators. The extension is important especially to express several aspects of signals that cannot be expressed in plain STL (e.g., presence of local extremes and their mutual relationships, non-trivial oscillatory behaviour such as damped oscillations, etc.). In this short paper, we address the tool Parasim that includes an implementation of the algorithm for computing robustness with respect to an STL* specification. The tool is in its current version considered as a prototype implementation of the algorithms for STL* robust monitoring of ODE models.

This work has been partially supported by the Czech Science Foundation grant No. 18-00178S.

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Notes

  1. 1.

    https://github.com/sybila/parasim/.

References

  1. Barkai, N., Leibler, S.: Robustness in simple biochemical networks. Nature 6636(387), 913–917 (1997)

    Article  Google Scholar 

  2. Bates, D.G., Cosentino, C.: Validation and invalidation of systems biology models using robustness analysis. IET Syst. Biol. 5(4), 229–244 (2011)

    Article  Google Scholar 

  3. Brim, L., Dluhoš, P., Šafránek, D., Vejpustek, T.: STL*: extending signal temporal logic with signal-value freezing operator. Inf. Comput. 236, 52–67 (2014)

    Article  MathSciNet  Google Scholar 

  4. Brim, L., Vejpustek, T., Šafránek, D., Fabriková, J.: Robustness analysis for value-freezing signal temporal logic. arXiv:1309.0867 (2013)

  5. Donzé, A.: Breach, a toolbox for verification and parameter synthesis of hybrid systems. In: Touili, T., Cook, B., Jackson, P. (eds.) CAV 2010. LNCS, vol. 6174, pp. 167–170. Springer, Heidelberg (2010). https://doi.org/10.1007/978-3-642-14295-6_17

    Chapter  Google Scholar 

  6. Donzé, A., Maler, O.: Robust satisfaction of temporal logic over real-valued signals. In: Chatterjee, K., Henzinger, T.A. (eds.) FORMATS 2010. LNCS, vol. 6246, pp. 92–106. Springer, Heidelberg (2010). https://doi.org/10.1007/978-3-642-15297-9_9

    Chapter  MATH  Google Scholar 

  7. Eaton, J.W., Bateman, D., Hauberg, S., Wehbring, R.: GNU Octave Version 3.8.1 Manual: A High-level Interactive Language for Numerical Computations. CreateSpace Independent Publishing Platform, Scotts Valley (2014)

    Google Scholar 

  8. Fainekos, G., Pappas, G.J.: Robustness of temporal logic specifications for continuous-time signals. Theoret. Comput. Sci. 410(42), 4262–4291 (2009)

    Article  MathSciNet  Google Scholar 

  9. Keller, R., et al.: The systems biology simulation core algorithm. BMC Syst. Biol. 7(1), 55 (2013)

    Article  Google Scholar 

  10. Rizk, A., Batt, G., Fages, F., Soliman, S.: A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics 25, 169–178 (2009)

    Article  Google Scholar 

  11. Steuer, R., Waldherr, S., Sourjik, V., Kollmann, M.: Robust signal processing in living cells. PLoS Comput. Biol. 7(11), e1002218 (2011)

    Article  MathSciNet  Google Scholar 

  12. Streif, S., et al.: Robustness analysis, prediction and estimation for uncertain biochemical networks. IFAC Proc. Volumes 46(32), 1–20 (2013)

    Article  Google Scholar 

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Correspondence to David Šafránek .

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Šafránek, D. et al. (2019). Barbaric Robustness Monitoring Revisited for STL* in Parasim. In: Bortolussi, L., Sanguinetti, G. (eds) Computational Methods in Systems Biology. CMSB 2019. Lecture Notes in Computer Science(), vol 11773. Springer, Cham. https://doi.org/10.1007/978-3-030-31304-3_26

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  • DOI: https://doi.org/10.1007/978-3-030-31304-3_26

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-31303-6

  • Online ISBN: 978-3-030-31304-3

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