Abstract
Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expands these capabilities to cover additional types of models, model languages, parameter estimations, simulations and analyses of models, and analyses and visualizations of simulation results. To facilitate consistent practices across the community, Level 1 Version 4 also more clearly describes the use of SED-ML constructs, and includes numerous concrete validation rules. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including eight languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, over 20 simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/.
Highlights
The efforts to standardize the representation of computational models in various areas of biology, such as the Systems Biology Markup Language (SBML) [16], CellML [9] or NeuroML [13], resulted in an increase of the exchange and re-use of models
Simulation Experiment Description Markup Language (SED-ML) can capture the information in the Minimum Information About a Simulation Experiment (MIASE) [22] guidelines
models to use (Model) languages can choose to use XPath to identify abstract concepts implied by models that are not defined in XML files, such as ‘the current value of the object corresponding to an XML element within the state of a simulation run’
Summary
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for describing simulation experiments, including model changes, calibrations, simulations, analyses, and computations and visualizations of simulation results. The efforts to standardize the representation of computational models in various areas of biology, such as the Systems Biology Markup Language (SBML) [16], CellML [9] or NeuroML [13], 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. We use a red color in text and a dark blue color in figures to indicate changes between this version of the specification, namely SED-ML Level 1 Version 4, and the most recent previous release of the specification (which, for the present case, is SED-ML Level 1 Version 3). When viewed in electronic form, clicking on blue-colored text will cause a jump to the section, figure, table or page to which the link refers
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