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Speeding Up Phylogenetic Model Checking

Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 222)

Abstract

Model checking is a generic and formal technique that the authors have proposed for the study of properties that emerge from the biological labeling of the states defined over the phylogenetic tree [3] [10]. This strategy allows us to use generic software tools already present in the industry. However, the performance of traditional model checking is penalized when scaling the system for large phylogenies. To this end, two strategies are presented here. The first one consists of partitioning the phylogenetic tree into a set of related subproblems so as to speed up the computation time and distribute the memory consumption. The second strategy is based on uncoupling the information associated to each state of the phylogenetic tree (mainly, the DNA sequence) and exporting it to an external tool for the management of large information systems. The integration of all these approaches outperformed the results of monolithic model checking and helped us to execute the verification of properties in a real phylogenetic tree.

Keywords

distributed and sliced model checking database phylogenetic property 

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References

  1. 1.
    Baier, C., Katoen, J.-P.: Principles of model checking. The MIT Press, Cambridge (2008)MATHGoogle Scholar
  2. 2.
    Benson, D.A., Karsch-Mizrachi, I., Clark, K., Lipman, D.J., Ostell, J., Sayers, E.W.: GenBank. Nucleic Acids Reseach 40, D48–D53 (2012)Google Scholar
  3. 3.
    Blanco, R., de Miguel Casado, G., Requeno, J.I., Colom, J.M.: Temporal logics for phylogenetic analysis via model checking. In: 2010 IEEE Int. Conf. on Bioinformatics and Biomedicine Workshops, pp. 152–157. IEEE (2010)Google Scholar
  4. 4.
    Blanco, R., Mayordomo, E., Montoya, J., Ruiz-Pesini, E.: Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge. BMC Bioinformatics 12, 174 (2011)CrossRefGoogle Scholar
  5. 5.
    Bošnački, D., Edelkamp, S.: Model checking software: on some new waves and some evergreens. Int. J. Software Tool Tech. Tran. 12, 89–95 (2010)CrossRefGoogle Scholar
  6. 6.
    Boukala, M.C., Petrucci, L.: Distributed CTL Model-Checking and counterexample search. In: 3rd Int. Workshop on Verification and Evaluation of Computer and Communication Systems (2009)Google Scholar
  7. 7.
    Cimatti, A., Clarke, E., Giunchiglia, E., Giunchiglia, F., Pistore, M., Roveri, M., Sebastiani, R., Tacchella, A.: NuSMV 2: An OpenSource Tool for Symbolic Model Checking. In: Brinksma, E., Larsen, K.G. (eds.) CAV 2002. LNCS, vol. 2404, pp. 359–364. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  8. 8.
    Fitch, W.M.: Uses for Evolutionary Trees. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 349, 93–102 (1995)CrossRefGoogle Scholar
  9. 9.
    Mangalam, H.: The Bio* toolkits a brief overview. Brief Bioinform. 3(3), 296–302 (2002)Google Scholar
  10. 10.
    Requeno, J.I., Blanco, R., de Miguel Casado, G., Colom, J.M.: Phylogenetic Analysis Using an SMV Tool. In: Rocha, M.P., Corchado Rodríguez, J.M., Fdez-Riverola, F., Valencia, A. (eds.) PACBB 2011. AISC, vol. 93, pp. 167–174. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  11. 11.
    Requeno, J.I., Blanco, R., de Miguel Casado, G., Colom, J.M.: Sliced Model Checking for Phylogenetic Analysis. In: Rocha, M.P., Luscombe, N., Fdez-Riverola, F., Corchado Rodríguez, J.M. (eds.) 6th International Conference on PACBB. AISC, vol. 154, pp. 95–104. Springer, Heidelberg (2012)CrossRefGoogle Scholar
  12. 12.
    Shegalov, G.: CTL Model Checking in Database Cloud. Unpublished version paper (2011)Google Scholar

Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  1. 1.Department of Computer Science and Systems Engineering (DIIS)Universidad de ZaragozaZaragozaSpain

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