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

Nicolas Rodriguez,Nicolas Le Novère,Marco Donizelli

doi:10.1186/1471-2105-8-79

Nicolas Rodriguez, Nicolas Le Novère + Show 1 more

Open Access

https://doi.org/10.1186/1471-2105-8-79

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Abstract

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

Highlights

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 is a fully functional editor for modellers who want to develop a model de novo in SBML, and for scientists who need to read an SBML model generated by another tool
SBMLeditor is used by the curators of BioModels Database [18] to encode models, or to curate models submitted to the database by third-parties

Summary

Results

SBMLeditor is written in JAVA using JCompneur, a library providing interfaces to 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

Background

Conclusion

17. Le Novère N