SBMLeditor: effective creation of models in the Systems Biology Markup Language SBMLReport as inadecuate




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BMC Bioinformatics

, 8:79

First Online: 06 March 2007Received: 30 November 2006Accepted: 06 March 2007

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.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-8-79 contains supplementary material, which is available to authorized users.

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Author: Nicolas Rodriguez - Marco Donizelli - Nicolas Le Novère

Source: https://link.springer.com/







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