CellPublisher is a free and open source program to make highly interactive representations of biochemical processes. It converts a file in the Systems Biology Markup Language (SBML) created with the popular modeling tool CellDesigner into an interactive Web application, which allows the user to explore the model and access detailed explanations of the model component enhanced with references to scientific publications, experimental data and modeling results. MIEP makes use of CellPublisher to disseminate the models developed in the program to the scientific community in a user friendly way.

Our Bioinformatics Team at the Nutritional Immunology and Molecular Medicine Laboratory and MIEP incorporated three major enhancements to CellPublisher. These improvements allow annotating reactions in addition to species, thereby allowing scientists to convey more information about the interactions in their models. The Google map markers are only shown for objects, which have been annotated. It is immediately visible to the user where information is available. This behavior is similar to the road maps one sees in Google. Another improvement is that the capability to display 3D protein structures through JMol has been enhanced by making it compatible with all major Web browsers on common operating systems. We also reduced the size of annotation markers so that they do not interfere with the network information conveyed through the graphic representation of the model.

The CellPublisher source code which we are using to create the annotated interactive model networks found on the is site is available at SourceForge. The enhancement can be retrieved directly form the repository with:

    svn co https://cellpublisher.svn.sourceforge.net/svnroot/cellpublisher/branchees/modelingimmunity.org