CMSB 2015: Computational Methods in Systems Biology pp 251-263 | Cite as
Parameter Synthesis by Parallel Coloured CTL Model Checking
Conference paper
First Online:
Abstract
We propose a new distributed-memory parallel algorithm for parameter synthesis from CTL hypotheses. The algorithm colours the state space transitions by different parameterisations and extends CTL model checking to identify the maximal set of parameters that guarantee the satisfaction of the given CTL property. We experimentally confirm good scalability of our approach and demonstrate its applicability in the case study of a genetic switch controlling decisions in the cell cycle.
References
- 1.Ballarini, P., Guido, R., Mazza, T., Prandi, D.: Taming the complexity of biological pathways through parallel computing. Brief. Bioinform 10(3), 278–288 (2009)CrossRefGoogle Scholar
- 2.Barnat, J., Brim, L., Krejci, A., Streck, A., Safranek, D., Vejnar, M., Vejpustek, T.: On parameter synthesis by parallel model checking. IEEE/ACM Trans. Comput. Bio. Bioinform. 9(3), 693–705 (2012)CrossRefGoogle Scholar
- 3.Barnat, J., Brim, L., Safránek, D.: High-performance analysis of biological systems dynamics with the divine model checker. Brief. Bioinform. 11(3), 301–312 (2010)CrossRefGoogle Scholar
- 4.Batt, G., Belta, C., Weiss, R.: Model checking liveness properties of genetic regulatory networks. In: Grumberg, O., Huth, M. (eds.) TACAS 2007. LNCS, vol. 4424, pp. 323–338. Springer, Heidelberg (2007) CrossRefGoogle Scholar
- 5.Batt, G., Page, M., Cantone, I., Gössler, G., Monteiro, P., de Jong, H.: Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. Bioinformatics 26(18), 603–610 (2010)CrossRefGoogle Scholar
- 6.Batt, G., Ropers, D., Jong, H.D., Geiselmann, J., Mateescu, R., Schneider, D.: Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in escherichia coli. Bioinformatics 21, 19–28 (2005)CrossRefGoogle Scholar
- 7.Brim, L., Češka, M., Šafránek, D.: Model checking of biological systems. In: Bernardo, M., de Vink, E., Di Pierro, A., Wiklicky, H. (eds.) SFM 2013. LNCS, vol. 7938, pp. 63–112. Springer, Heidelberg (2013) CrossRefGoogle Scholar
- 8.Brim, L., Yorav, K., Zidkova, J.: Assumption-based distribution of CTL model checking. STTT 7(1), 61–73 (2005)CrossRefGoogle Scholar
- 9.Clarke, E.M., Emerson, E.A., Sistla, A.P.: Automatic verification of finite-state concurrent systems using temporal logic specifications. ACM Trans. Program. Lang. Syst. 8, 244–263 (1986)CrossRefMATHGoogle Scholar
- 10.Collins, P., Habets, L.C., van Schuppen, J.H., Černá, I., Fabriková, J., Šafránek, D.: Abstraction of biochemical reaction systems on polytopes. In: IFAC World Congress, pp. 14869–14875. IFAC (2011)Google Scholar
- 11.Donaldson, R., Gilbert, D.: A model checking approach to the parameter estimation of biochemical pathways. In: Heiner, M., Uhrmacher, A.M. (eds.) CMSB 2008. LNCS (LNBI), vol. 5307, pp. 269–287. Springer, Heidelberg (2008) CrossRefGoogle Scholar
- 12.Donzé, A., Clermont, G., Langmead, C.J.: Parameter synthesis in nonlinear dynamical systems: application to systems biology. J. Comput. Biol. 17(3), 325–336 (2010)MathSciNetCrossRefGoogle Scholar
- 13.Donzé, A., Fanchon, E., Gattepaille, L.M., Maler, O., Tracqui, P.: Robustness analysis and behavior discrimination in enzymatic reaction networks. PLoS ONE 6(9), e24246 (2011)CrossRefGoogle Scholar
- 14.Fages, F., Soliman, S.: Formal cell biology in biocham. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 54–80. Springer, Heidelberg (2008) CrossRefGoogle Scholar
- 15.Fröhlich, F., Theis, F.J., Hasenauer, J.: Uncertainty analysis for non-identifiable dynamical systems: profile likelihoods, bootstrapping and more. In: Mendes, P., Dada, J.O., Smallbone, K. (eds.) CMSB 2014. LNCS, vol. 8859, pp. 61–72. Springer, Heidelberg (2014) Google Scholar
- 16.Gábor, A., Banga, J.R.: Improved parameter estimation in kinetic models: selection and tuning of regularization methods. In: Mendes, P., Dada, J.O., Smallbone, K. (eds.) CMSB 2014. LNCS, vol. 8859, pp. 45–60. Springer, Heidelberg (2014) Google Scholar
- 17.Gilbert, D., Breitling, R., Heiner, M., Donaldson, R.: An introduction to biomodel engineering, illustrated for signal transduction pathways. In: Corne, D.W., Frisco, P., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2008. LNCS, vol. 5391, pp. 13–28. Springer, Heidelberg (2009) CrossRefGoogle Scholar
- 18.Grosu, R., Batt, G., Fenton, F.H., Glimm, J., Le Guernic, C., Smolka, S.A., Bartocci, E.: From cardiac cells to genetic regulatory networks. In: Gopalakrishnan, G., Qadeer, S. (eds.) CAV 2011. LNCS, vol. 6806, pp. 396–411. Springer, Heidelberg (2011) CrossRefGoogle Scholar
- 19.Jha, S.K., Langmead, C.J.: Synthesis and infeasibility analysis for stochastic models of biochemical systems using statistical model checking and abstraction refinement. Theor. Comput. Sci. 412(21), 2162–2187 (2011)MathSciNetCrossRefMATHGoogle Scholar
- 20.Jha, S., Shyamasundar, R.K.: Adapting biochemical kripke structures for distributed model checking. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 107–122. Springer, Heidelberg (2006) CrossRefGoogle Scholar
- 21.Liu, B., Kong, S., Gao, S., Zuliani, P., Clarke, E.M.: Parameter synthesis for cardiac cell hybrid models using \(\delta \)-decisions. In: Mendes, P., Dada, J.O., Smallbone, K. (eds.) CMSB 2014. LNCS, vol. 8859, pp. 99–113. Springer, Heidelberg (2014) Google Scholar
- 22.Mittnacht, S.: Control of prb phosphorylation. Curr. Opin. Genet. Dev. 8(1), 21–27 (1998)CrossRefGoogle Scholar
- 23.Monteiro, P.T., Ropers, D., Mateescu, R., Freitas, A.T., de Jong, H.: Temporal logic patterns for querying qualitative models of genetic regulatory networks. In: ECAI. FAIA, vol. 178, pp. 229–233. IOS Press (2008)Google Scholar
- 24.Raue, A., Karlsson, J., Saccomani, M.P., Jirstrand, M., Timmer, J.: Comparison of approaches for parameter identifiability analysis of biological systems. Bioinformatics 30, 1440–1448 (2014)CrossRefGoogle Scholar
- 25.Rizk, A., Batt, G., Fages, F., Soliman, S.: A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics 25(12), 169–178 (2009)CrossRefGoogle Scholar
- 26.Swat, M., Kel, A., Herzel, H.: Bifurcation analysis of the regulatory modules of the mammalian G1/S transition. Bioinformatics 20(10), 1506–1511 (2004)CrossRefGoogle Scholar
Copyright information
© Springer International Publishing Switzerland 2015