SED-ED, a workflow editor for computational biology experiments written in SED-ML

Bioinformatics. 2012 Apr 15;28(8):1180-1. doi: 10.1093/bioinformatics/bts101. Epub 2012 Feb 25.


The simulation experiment description markup language (SED-ML) is a new community data standard to encode computational biology experiments in a computer-readable XML format. Its widespread adoption will require the development of software support to work with SED-ML files. Here, we describe a software tool, SED-ED, to view, edit, validate and annotate SED-ML documents while shielding end-users from the underlying XML representation. SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format.

Availability and implementation: SED-ED is available as a standalone Java application, as an Eclipse plug-in and as an SBSI ( plug-in, all under an MIT open-source license. Source code is at The application itself is available from

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Humans
  • Models, Biological*
  • Programming Languages
  • Software*
  • Systems Biology / methods
  • User-Computer Interface
  • Workflow