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SED-ML – An XML Format for the Implementation of the MIASE Guidelines

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 5307)

Abstract

Share and reuse of biochemical models have become two of the main issues in the field of Computational Systems Biology. There already exist widely-accepted formats to encode the structure of models. However, the problem of describing the simulations to be run using those models has not yet been tackled in a satisfactory way. The community believes that providing detailed information about simulation recipes will highly improve the efficient use of existing models. Accordingly a set of guidelines called the Minimum Information About a Simulation Experiment (MIASE) is currently under development. It covers information about the simulation settings, including information about the models, changes on them, simulation settings applied to the models and output definitions. Here we present the Simulation Experiment Description Markup Language (SED-ML), an XML format that enables the storage and exchange of part of the information required to implement the MIASE guidelines. SED-ML is independent of the formats used to encode the models – as long as they are expressed in XML –, and it is independent of the software tools used to run the simulations. Several test implementations are being developed to benchmark SED-ML on simple cases, and pave the way to a more complete support of MIASE.

Keywords

  • Resource Description Framework
  • Simulation Algorithm
  • Simulation Setting
  • System Biology Markup Language
  • XPath Expression

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.

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References

  1. Le Novère, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J., Spence, H., Wanner, B.: Minimum Information Requested In the Annotation of biochemical Models (MIRIAM). Nature Biotechnology 23(12), 1509–1515 (2005)

    CrossRef  PubMed  Google Scholar 

  2. Hucka, M., Bolouri, H., Finney, A., Sauro, H., Doyle, J., Kitano, H., Arkin, A., Bornstein, B., Bray, D., Cuellar, A., Dronov, S., Ginkel, M., Gor, V., Goryanin, I., Hedley, W., Hodgman, T., Hunter, P., Juty, N., Kasberger, J., Kremling, A., Kummer, U., Le Novère, N., Loew, L., Lucio, D., Mendes, P., Mjolsness, E., Nakayama, Y., Nelson, M., Nielsen, P., Sakurada, T., Schaff, J., Shapiro, B., Shimizu, T., Spence, H., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., Wang, J.: The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003)

    CAS  CrossRef  PubMed  Google Scholar 

  3. Lloyd, C., Halstead, M., Nielsen, P.: CellML: its future, present and past. Progress in Biophysics & Molecular Biology 85, 433–450 (2004)

    CAS  CrossRef  Google Scholar 

  4. Object Management Group (OMG): Unified Modeling Language (UML), Version 2.1.2 (2007), http://www.omg.org/spec/UML/2.1.2/

  5. Ausbrooks, R., Buswell, S., Carlisle, D., Dalmas, S., Devitt, S., Diaz, A., Froumentin, M., Hunter, R., Ion, P., Kohlhase, M., Miner, R., Poppelier, N., Smith, B., Soiffer, N., Sutor, R., Watt, S.: Mathematical Markup Language (MathML) Version 2.0, 2nd edn. (2003)

    Google Scholar 

  6. World Wide Web Consortium (W3C) Recommendation: XML Path Language (XPath) (1999), http://www.w3.org/TR/xpath

  7. Köhn, D., Le Novère, N.: The Kinetic Simulation Algorithm Ontology (KiSAO). Website (2007), http://www.ebi.ac.uk/compneur-srv/kisao/

  8. Leloup, J., Goldbeter, A.: Chaos and birhythmicity in a model for circadian oscillations of the per and tim proteins in drosophila. Journal of theoretical biology 198(3), 445–459 (1999)

    CAS  CrossRef  PubMed  Google Scholar 

  9. Le Novère, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J., Hucka, M.: Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34(Database issue) (January 2006)

    Google Scholar 

  10. Hoops, S., Sahle, S., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., Kummer, U.: Copasi a complex pathway simulator. Bioinformatics 22(24), 3067–3074 (2006)

    CAS  CrossRef  PubMed  Google Scholar 

  11. Miller, A.: CellML simulation metadata specification – a specification for simulation metadata (2007), http://www.cellml.org/specifications/metadata/simulations

  12. World Wide Web Consortium (W3C) Recommendation: Resource Description Framework (RDF) (1997), http://www.w3.org/RDF

  13. Kopalov, F.: SBML extensions for level 3: Experiments, simulation, parameters, results and plots (March 2008) (unpublished proposal)

    Google Scholar 

  14. World Wide Web Consortium (W3C) Specification: Document Type Definition (DTD) (1998), http://www.w3.org/XML/1998/06/xmlspec-report

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Köhn, D., Le Novère, N. (2008). SED-ML – An XML Format for the Implementation of the MIASE Guidelines. In: Heiner, M., Uhrmacher, A.M. (eds) Computational Methods in Systems Biology. CMSB 2008. Lecture Notes in Computer Science(), vol 5307. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88562-7_15

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  • DOI: https://doi.org/10.1007/978-3-540-88562-7_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-88561-0

  • Online ISBN: 978-3-540-88562-7

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