SBML is one of the most popular modeling and data exchange languages in systems biology. A very popular software application in systems biology is CellDesigner. Long before the SBML extensions for Layout and Rendering were defined, CellDesigner already provided mechanisms to display network diagrams and store them inside SBML files. To achieve this, the developers of CellDesigner created their own SBML annotations. It would be useful if a standalone parser existed that could convert files in CellDesigner's SBML dialect into SBML Level 3 format using the SBML Level 3 Layout and Rendering packages.
Goal
Implement a standalone conversion program that can convert CellDesigner's unique SBML-based diagrams into official SBML Level 3 format. Time permitting, the result could be integrated into the Systems Biology Format Converter (SBFC).
Technologies
SBML, possibly Java (with the help of JSBML) or possibly other languages (with the help of libSBML). A skeleton for format converters exists in the form of the Systems Biology Format Converter (SBFC) system, and some portions of that could be used to help implement this CellDesigner format converter.
Potential Mentors
Andreas Dräger, Akira Funahashi, Nicolas Rodriguez.
khanspers
commented
8 years ago
Background
SBML is one of the most popular modeling and data exchange languages in systems biology. A very popular software application in systems biology is CellDesigner. Long before the SBML extensions for Layout and Rendering were defined, CellDesigner already provided mechanisms to display network diagrams and store them inside SBML files. To achieve this, the developers of CellDesigner created their own SBML annotations. It would be useful if a standalone parser existed that could convert files in CellDesigner's SBML dialect into SBML Level 3 format using the SBML Level 3 Layout and Rendering packages.
Goal
Implement a standalone conversion program that can convert CellDesigner's unique SBML-based diagrams into official SBML Level 3 format. Time permitting, the result could be integrated into the Systems Biology Format Converter (SBFC).
Technologies
SBML, possibly Java (with the help of JSBML) or possibly other languages (with the help of libSBML). A skeleton for format converters exists in the form of the Systems Biology Format Converter (SBFC) system, and some portions of that could be used to help implement this CellDesigner format converter.
Potential Mentors
Andreas Dräger, Akira Funahashi, Nicolas Rodriguez.
Contact
SBML Team
Useful pointers to documentation related to GSOC for student on the main NRNB web site :