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

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.SBMLeditor contains many improvements compared to a generic XML editor, and allow users to create an SBML model quickly and without syntactic errors.In Systems Biology, complementary computational tools are often used to model and analyse different characteristics of a particular system. Most tools have their own specific format for entering and storing models, and switching tools not long ago most often required re-writing the model from scratch. Moreover, when a tool was no longer supported, models could be lost forever.The Systems Biology Markup Language (SBML) is a free, open, XML-based format designed to promote interoperability between different tools [1]. Model descriptions produced by one tool can be read and processed by other programs. It also offers a standard representation for model storage, transmission, and re-use. SBML can be used for describing models of (but not restricted to) signalling pathways, metabolic networks, gene regulation networks, etc. SBML is specified as a set of class descriptions, and can be implemented in very different ways. Currently it is mainly instantiated as an XML language [2].Although SBML is text-based, and can be edited in a simple text editor, it is intended to be written and read by machines, not by human beings. As such, it requires specific user-interfaces to translate modeller's intentions into its computer representation.The main target users of this SBML editor ar