Advertisement

Phylogenetic Analysis Using an SMV Tool

  • José Ignacio Requeno
  • Roberto Blanco
  • Gregorio de Miguel Casado
  • José Manuel Colom
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 93)

Abstract

The need for general methods to verify biological properties in phylogenetics motivates research in formal frameworks so that biologists can focus their efforts exclusively in evolution modeling and property specification. Model checking is proposed to this end. Three pillars found this approach: modeling evolution dynamics as transition systems; specifying phylogenetic properties using temporal logic formulae; and verifying the former by means of automated computer tools. As prominent advantages for studying biological properties under our approach, different models of evolution can be considered, complex properties can be specified as the logical composition of others, and the refinement of unfulfilled properties as well as the discovery of new ones can be undertaken by exploiting the results of verification. Preliminary experimental results using the Cadence Symbolic Model Verifier support the feasibility of the methodology.

Keywords

Model Check Temporal Logic Computation Tree Atomic Proposition Kripke Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Baier, C., Katoen, J.-P.: Principles of model checking. The MIT Press, Cambridge (2008)zbMATHGoogle Scholar
  2. 2.
    Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Sayers, E.W.: GenBank. Nucleic Acids Res. 38, D46–D51 (2010)CrossRefGoogle Scholar
  3. 3.
    Blanco, R., de Miguel Casado, G., Requeno, J.I., Colom, J.M.: Temporal logics for phylogenetic analysis via model checking. In: Proceedings of the IEEE International Workshop on Mining and Management of Biological and Health Data. IEEE, Los Alamitos (2010) (in press)Google Scholar
  4. 4.
    Clarke, E.M., Emerson, E.A.: Design and synthesis of synchronization skeletons using branching time temporal logic. In: Kozen, D. (ed.) Logics of Programs, pp. 52–71. Springer, Heidelberg (1982)CrossRefGoogle Scholar
  5. 5.
    Felsenstein, J.: Inferring phylogenies. Sinauer, Sunderland (2003)Google Scholar
  6. 6.
    Manna, Z., Pnueli, A.: The temporal logic of reactive and concurrent systems: specification. Springer, Berlin (1991)zbMATHGoogle Scholar
  7. 7.
    McMillan, K.L.: A methodology for hardware verification using compositional model checking. Sci. Comput. Program 37, 279–309 (2000)zbMATHCrossRefGoogle Scholar
  8. 8.
    Montoya, J., López-Gallardo, E., Díez-Sánchez, C., López-Pérez, M.J., Ruiz-Pesini, E.: 20 years of human mtDNA pathologic point mutations: carefully reading the pathogenicity criteria. Biochim. Biophys. Acta 1787, 476–483 (2009)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • José Ignacio Requeno
    • 1
  • Roberto Blanco
    • 1
  • Gregorio de Miguel Casado
    • 1
  • José Manuel Colom
    • 1
  1. 1.Department of Computer Science and Systems Engineering (DIIS)/Aragon Institute of Engineering Research (I3A)Universidad de ZaragozaZaragozaSpain

Personalised recommendations