Advertisement

A Mozart Implementation of CP(BioNet)

  • Grégoire Dooms
  • Yves Deville
  • Pierre Dupont
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3389)

Abstract

The analysis of biochemical networks consists in studying the interactions between biological entities cooperating in complex cellular processes. To facilitate the expression of analyses and their computation, we introduced CP(BioNet), a constraint programming framework for the analysis of biochemical networks. An Oz-Mozart prototype of CP(BioNet) is described. This prototype consists of the implementation of a new kind of domain variables, graph domain variables, and the implementation of constraint propagators for constraints over graph-domain variables. These new variables and constraints are implemented in Oz and they can then be used like other domain variables in the Oz-Mozart platform. An implementation of a path constraint propagator is described in depth and constrained path finding tests are analysed to assess the tractability of our approach. Finally, an alternative Oz-Mozart data-structure for the graph-domain variables is presented and compared to the first one.

Keywords

Mozart Oz Constraint Programming Graph Domain Variables Constrained Path Finding Path Constraint 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    The aMAZE data-base project, http://www.amaze.ulb.ac.be/
  2. 2.
    Bader, G.D., Donaldson, I., Wolting, C., Ouellette, B.F., Pawson, T., Hogue, C.W.: Bind the biomolecular interaction network database. Nucleic Acids Research 29(1), 242–245 (2001)CrossRefGoogle Scholar
  3. 3.
    Cohen, J.: Théorie des graphes et algorithmes. Course notes, http://www.univ-paris12.fr/lacl/cohen/poly_gr.ps
  4. 4.
    Dooms, G., Deville, Y., Dupont, P.: Constrained path finding in biochemical networks. In: Proceedings of JOBIM 2004, p. 40 (2004)Google Scholar
  5. 5.
    Dooms, G., Deville, Y., Dupont, P.: Recherche de chemins contraints dans les réseaux biochimiques. In: Mesnard, F. (ed.) Programmation en logique avec contraintes, actes des JFPLC 2004, pp. 109–128. Hermes Science (2004)Google Scholar
  6. 6.
    Ellis, L.B.M., Hou, B.K., Kang, W., Wackett, L.P.: Wackett. The university of minesota biocatalysis/biodegradation database: post-genomic data mining. Nucleic Acids Research 31(1), 262–265 (2002)CrossRefGoogle Scholar
  7. 7.
    EMP project. Informations about EMP can be found at, http://www.empproject.com/
  8. 8.
    Gondran, M., Minoux, M.: Graphes et algorithmes. Eyrolles, 3éme éd (1995)Google Scholar
  9. 9.
    Goto, S., Nishioka, T., Kanehisa, M.: LIGAND: Chemical database for enzyme reactions. Bioinformatics 14, 591–599 (1998)CrossRefGoogle Scholar
  10. 10.
    Gross, J., Yellen, J.: Graph Theory and its Applications. CRC Press, Boca Raton (1999)zbMATHGoogle Scholar
  11. 11.
    Holm, J., de Lichtenberg, K., Thorup, M.: Poly-logarithmic deterministic fully-dynamic algorithms for connectivity, minimum spanning tree, 2-edge, and biconnectivity. Journal ACM 48(4), 723–760 (2001)zbMATHCrossRefGoogle Scholar
  12. 12.
    Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pelligrini-Toole, A., Bonavides, C., Gama-Castro, S.: The EcoCyc database. Nucleic Acids Research 30(1), 56–58 (2002)Google Scholar
  13. 13.
    Lemer, C., Antezana, E., Couche, F., Fays, F., Santolaria, X., Janky, R., Deville, Y., Richelle, J., Wodak, S.J.: The aMAZE lightbench: a web interface to a relational database of cellular processes. Nucleic Acids Research 32, D443–D448 (2004)CrossRefGoogle Scholar
  14. 14.
    Minoru, K., Susumu, G., Shuichi, K., Akihiro, N.: The KEGG databases at GenomeNet. Nucleic Acids Research 30(1), 42–46 (2002)CrossRefGoogle Scholar
  15. 15.
    Schilkey, F.: PathDB: a pathway database, http://www.ncgr.org/pathdb
  16. 16.
    Takai-Igarashi, T., Kaminuma, T.: A pathway finding system for the cell signaling networks database. Silico Biology 1, 129–146 (1999)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Grégoire Dooms
    • 1
  • Yves Deville
    • 1
  • Pierre Dupont
    • 1
  1. 1.Computing Science and Engineering DepartmentUniversité catholique de LouvainLouvain-la-NeuveBelgium

Personalised recommendations