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Computational Methods in Systems Biology

Volume 5307 of the series Lecture Notes in Computer Science pp 176-190

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

  • Dagmar KöhnAffiliated withResearch Training School dIEM oSiRiS, University of Rostock
  • , Nicolas Le NovèreAffiliated withEuropean Bioinformatics Institute

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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.