Abstract
The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.
Highlights
The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as Systems Biology Markup Language (SBML) or CellML standardize the formal representation of computational models in various areas of biology
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported
The efforts to standardize the representation of computational models in various areas of biology, such as the Systems Biology Markup Language (SBML) [14], CellML [8] or NeuroML [11], resulted in an increase of the exchange and re-use of models
Summary
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for the description of simulation experiments. The efforts to standardize the representation of computational models in various areas of biology, such as the Systems Biology Markup Language (SBML) [14], CellML [8] or NeuroML [11], resulted in an increase of the exchange and re-use of models. The increasing use of computational simulation experiments to inform modern biological research creates new challenges to reproduce, annotate, archive, and share such experiments. SED-ML describes in a computer-readable exchange format the information for the reproduction of simulation experiments. SED-ML is a software-independent format encoded in XML not specific to particular simulation tools and independent of the underlying model language. This document describes Level 1 Version 3 of SED-ML which is the successor of Level 1 Version 2 and Level 1 Version 1 (described in [20])
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