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Towards a Scientific Model Management System

  • Fabio Porto
  • José Antônio de Macedo
  • Javier Sanchez Tamargo
  • Yuanjian Wang Zufferey
  • Vânia P. Vidal
  • Stefano Spaccapietra
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5232)

Abstract

Computational models of biological systems aim at accurately simulating in vivo phenomena. They have become a very powerful tool enabling scientists to study complex behavior. A side effect of their success unfortunately exists and is observed as an increasing difficulty in managing data, metadata and a myriad of programs and tools used and produced during a research task. In this work we aim at supporting scientists during a research endeavour by using Scientific Models as a main guiding element for describing, searching and running computational models, as well as managing the corresponding results. We assume a data-oriented perspective for scientific model representation materialized into a data model with which users describe scientific models and corresponding computational models, and a query language with which a scientist specifies simulation queries. The model is grounded in XML and tightly related to domain ontologies, which provide formal domain descriptions and uniform terminology. Scientists may search for scientific models and run simulations that automatically invoke the underlying programs on provided inputs. The results of a simulation may generate complex data that can be queried in the context of the scientific model. Higher-level models can be specified through views that export a unified representation of underlying scientific models.

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References

  1. 1.
    Hunter, J.: Scientific Models – A User-oriented Approach to the Integration of Scientific Data and Digital Libraries. In: VALA 2006, Melbourne (February 2006)Google Scholar
  2. 2.
    Jaqaman, K., Danuser, G.: Linking data to models: data regression. Nature Reviews, Molecular Cell Biology V(7), 813–819 (2006)CrossRefGoogle Scholar
  3. 3.
    Silvert, W.: Modelling as a discipline. International Journal General Systems V30(3), 1–22 (2000)zbMATHGoogle Scholar
  4. 4.
    Oinn, T., Greenwood, M., Addis, M.: Taverna: Lessons in creating a workflow envi-ronment for the life sciences. Concurrence Computation: Pract. Exper., 1–7 (2000)Google Scholar
  5. 5.
    Akram, A., Meredith, D., Allan, R.: Evaluation of BPEL for Scientific Workflows. Cluster Computing and the Grid, CCGRID V1(16-19) (2006)Google Scholar
  6. 6.
  7. 7.
    Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludascher, B., Kepler, M.: An Extensible System for Design and Execution of Scientific Workflows. In: SSDBM (2004)Google Scholar
  8. 8.
    MATLAB (last access, 24/06/2008), http://en.wikipedia.org/wiki/Matlab
  9. 9.
    Neuron (last access, 24/06/2008), http://www.neuron.yale.edu
  10. 10.
    Roure, D., Goble, C., Stevens, R.: Designing the myExperiment Virtual Research Envi-ronment for the Social Sharing of Workflows. In: e-Science 2007 - Third IEEE Int. Conf. on e-Science and Grid Computing, Bangalore, India, December 10-13, 2007, pp. 603–610 (2007)Google Scholar
  11. 11.
    Porto, F., Tajmouati, O., Silva, V., Schulze, B., Ayres, F.: QEF - Supporting Complex Query Applications. In: CCGRID 2007, Rio de Janeiro, Brazil, pp. 846–851 (2007)Google Scholar
  12. 12.
    Kandel, E., Schwarts, J., Jessel, T.: Principles of NeuroScience, 4th edn. McGraw-Hill, New York (2000)Google Scholar
  13. 13.
    Hodgkin, A., Huxley, A.: A quantitative description of ion currents and its applications to conduction and excitation in nerve membranes. J. Physiol (Lond.) 117, 500–544 (1952)CrossRefGoogle Scholar
  14. 14.
    (last accessed, 26/04/2008), http://lsids.sourceforge.net/
  15. 15.
    Grosof, B., Horrocks, I., Volz, R., Decker, S.: Description Logic Programs: Combining Logic Programs with Description Logic. In: Proc. WWW 2003, Budapest (May 2003)Google Scholar
  16. 16.
    (last accessed, 26/04/2008), http://www.w3.org/TR/xpath
  17. 17.
    Elmasri, R., Navathe, S.: Fundamentals of Database Systems, 2nd edn. Benjamin/Cummings (1994)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Fabio Porto
    • 1
  • José Antônio de Macedo
    • 1
  • Javier Sanchez Tamargo
    • 1
  • Yuanjian Wang Zufferey
    • 1
  • Vânia P. Vidal
    • 2
  • Stefano Spaccapietra
    • 1
  1. 1.EPFL-IC – Database LaboratoryLausanneSwitzerland
  2. 2.UFC - Department of ComputingCearáBrazil

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