CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems

  • Sylvain Soliman
  • François Fages
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3082)

Abstract

We present CMBSlib, a library of Computational Models of Biological Systems. It is aimed at providing a list of test problems for formalisms, modeling issues and implementation issues in systems biology.

The main motivation for CMBSlib is to stimulate research on the formal modeling of biological systems, by facilitating the exchange of formal models between researchers, and by providing a forum of comparison and validation of not only models, but also modeling formalisms and implementations.

Unlike a standardization effort, CMBSlib welcomes the most exotic formalisms and models provided they attack the modeling of well documented biological systems. Models of biological systems written in any referenced formalism can be submitted to CMBSlib. No special format or standard is required.

We discuss the advantages of and problems encountered in building such a library, give an example of typical entry in the library, and most of all we invite the community to become active contributors to CMBSlib.

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References

  1. 1.
    Shapiro, B.E., Levchenko, A., Meyerowitz, E.M., Wold, B.J., Mjolsness, E.D.: Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 19, 677–678 (2003), http://www-aig.jpl.nasa.gov/public/mls/cellerator/ CrossRefGoogle Scholar
  2. 2.
    Regev, A., Silverman, W., Shapiro, E.Y.: Representation and simulation of biochemical processes using the pi-calculus process algebra. In: Proceedings of the sixth Pacific Symposium of Biocomputing, pp. 459–470 (2001)Google Scholar
  3. 3.
    ARC CPBIO: Process calculi and biology of molecular networks (2002–2003), http://contraintes.inria.fr/cpbio/
  4. 4.
    Gent, I.P., Walsh, T.: CSPLIB: A benchmark library for constraints. In: Jaffar, J. (ed.) CP 1999. LNCS, vol. 1713, pp. 480–481. Springer, Heidelberg (1999) (A longer version appeared as technical Report TR-APES-09-1999)Google Scholar
  5. 5.
    Chabrier, N., Chiaverini, M., Danos, V., Fages, F., Schächter, V.: Modeling and querying biochemical networks. Theoretical Computer Science (to appear, 2004)Google Scholar
  6. 6.
    Chabrier-Rivier, N., Fages, F., Soliman, S.: The biochemical abstract machine BIOCHAM. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 172–191. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  7. 7.
    Chabrier, N., Fages, F., Soliman, S.: BIOCHAM’s user manual. INRIA (2003–2004), http://contraintes.inria.fr/BIOCHAM/
  8. 8.
    Kohn, K.W.: Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Molecular Biology of Cell 10, 2703–2734 (1999)CrossRefGoogle Scholar
  9. 9.
    Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., Sönmez, M.K.: Pathway logic: Symbolic analysis of biological signaling. In: Proceedings of the seventh Pacific Symposium on Biocomputing, pp. 400–412 (2002)Google Scholar
  10. 10.
    Kanehisa, M., Goto, S.: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28, 27–30 (2000)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Sylvain Soliman
    • 1
  • François Fages
    • 1
  1. 1.Projet Contraintes, INRIA RocquencourtLe ChesnayFrance

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