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

Area of Science:

• Computational Biology
• Bioinformatics
• Scientific Software Development

Background:

• Simulation Experiment Description Markup Language (SED-ML) is a standard for encoding computational biology experiments.
• Widespread adoption of SED-ML requires accessible software tools for users.
• Existing methods for working with SED-ML files can be complex due to their XML format.

Purpose of the Study:

• To introduce SED-ED, a user-friendly software tool for viewing, editing, validating, and annotating SED-ML documents.
• To abstract the underlying XML complexity of SED-ML files for end-users.
• To support computational biologists in creating, understanding, and developing simulation descriptions.

Main Methods:

• SED-ED is implemented as a standalone Java application.
• SED-ED is available as a plug-in for the Eclipse Integrated Development Environment (IDE).
• SED-ED is also offered as a plug-in for the SBSI platform.

Main Results:

• SED-ED provides an intuitive interface for managing SED-ML documents.
• The tool shields users from the complexities of the XML structure.
• It facilitates the creation and modification of simulation experiment descriptions.

Conclusions:

• SED-ED enhances the usability of the SED-ML standard for computational modellers.
• The software promotes wider adoption and application of SED-ML in biological research.
• Open-source availability encourages community contribution and further development.