Simulation Experiment Description Markup Language

The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments. SED-ML allows to define the models to use, the experimental tasks to run and which results to produce.

Normative definitions

SED-ML is defined in a specification document that describes the elements of the language, its syntax, and provides validation rules.

The latest specification is SED-ML Level 1 Version 2.

A draft proposal is available for SED-ML Level 1 Version 3.

Governance

SED-ML development is coordinated by an editorial board elected by the community.

Communication

SED-ML development is discussed on the mailing list sed-ml-discuss@googlegroups.com.

Software support

Several software tools support SED-ML. Implementation of support is facilitated by a number of APIs.

Contact

For information about SED-ML itself, contact sed-ml-discuss@googlegroups.com. For information about SED-ML development and governance, contact sed-ml-editors@googlegroups.com. More information can be found on the SED-ML website: http://sed-ml.org

How to cite SED-ML

Waltemath D., Adams R., Bergmann F.T., Hucka M., Kolpakov F., Miller A.K., Moraru I.I., Nickerson D., Sahle S., Snoep J.L., Le Novère N. Reproducible computational biology experiments with SED-ML -- The Simulation Experiment Description Markup Language. BMC Systems Biology (2011), 5:198. http://identifiers.org/pubmed/22172142

History

The idea of developing a standard format for simulation experiment encoding was born at the European Bioinformatics Institute. In 2007, Dagmar Waltemath and Nicolas Le Novere started to draft such a format during Dagmar's Marie-Curie funded internship in the Compneur group.

The SED-ML project was first presented publicly at the 12^th SBML Forum Meeting in 2007, in Long Beach (US). The first version of SED-ML was then presented at the "Super-hackathon "standards and ontologies for Systems Biology"" in Okinawa in 2008. Back then, the language was called MIASE-ML. In Okinawa, many researchers showed a high interest in the format, and discussions were vital. MIASE became the Minimum Information guideline for simulation experiments. MIASE-ML was renamed into "Simulation Experiment Description Markup Language" (SED-ML).

Level 1 Version 1 of SED-ML officially appeared in March 2011, but SED-ML was presented, discussed and further specified during several community meetings in the years in between, including the combined "CellML-SBGN-SBO-BioPAX-MIASE workshop" in 2009, or the "2010 SBML-BioModels.net Hackathon".

Level 1 Version 2 of SED-ML was officially released on December 2, 2013 after two years of ratification by the community.

Since then SED-ML has been developed in collaboration with the communities forming the "computational modeling in biology network" (COMBINE). Besides dedicated sessions at various meetings, the development of SED-ML benefits from community interactions on the sed-ml-discuss mailing list (https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss/).