Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

Dagmar Waltemath,Richard Adams,Ion I Moraru,Jacky L Snoep,Nicolas Le Novère,Sven Sahle,Andrew K Miller,Michael Hucka,Fedor Kolpakov,David Nickerson,Frank T Bergmann

doi:10.1186/1752-0509-5-198

Abstract

BackgroundThe increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools.ResultsIn this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions.ConclusionsWith SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

Highlights

Circadian oscillations, of about 24 hr period, occur in most living organisms, and are among the most conspicuous biological rhythms
Simulation Experiment Description Markup Language (SED-ML) encodes the description of simulation experiments in XML, in an exchangeable, reusable manner
End-users might in addition share their own simulation experiment descriptions by exporting SED-ML from their simulation tool

Summary

Introduction

Of about 24 hr period, occur in most living organisms, and are among the most conspicuous biological rhythms. Different data formats have been developed to support the encoding of computational models of biological systems Such model representation formats include, for example, SBML [3], CellML [4] and NeuroML [5]. While these formats are widely accepted and used to describe model structure, they do not cover the description of simulation, or analyses performed with the models. To address this need, we created the Simulation Experiment Description Markup Language (SEDML, http://sed-ml.org/), an XML-based format for the encoding of simulation experiments performed on a set of computational models. We describe SED-ML and its development process as a community project in detail

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