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Open Access Software

SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)

Nicolas Rodriguez, Marco Donizelli and Nicolas Le Novère*

Author affiliations

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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Citation and License

BMC Bioinformatics 2007, 8:79  doi:10.1186/1471-2105-8-79

Published: 6 March 2007

Abstract

Background

The need to build a tool to facilitate the quick creation and editing of models encoded in the Systems Biology Markup language (SBML) has been growing with the number of users and the increased complexity of the language. SBMLeditor tries to answer this need by providing a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file.

Results

SBMLeditor is written in JAVA using JCompneur, a library providing interfaces to easily display an XML document as a tree. This decreases dramatically the development time for a new XML editor. The possibility to include custom dialogs for different tags allows a lot of freedom for the editing and validation of the document. In addition to Xerces, SBMLeditor uses libSBML to check the validity and consistency of SBML files. A graphical equation editor allows an easy manipulation of MathML. SBMLeditor can be used as a module of the Systems Biology Workbench.

Conclusion

SBMLeditor contains many improvements compared to a generic XML editor, and allow users to create an SBML model quickly and without syntactic errors.