CellDesigner is a modeling/simulating software capable of visualizing, modeling, and simulating gene­regulatory and biochemical networks. The key characteristics of CellDesigner are the solidly defined and comprehensive graphical representation of network models and systems biology markup language(SBML) as a model­ describing basis. However, these two characteristics contradict each other. SBML has a standardized definition for layout of network diagram. Before this was standardized, CellDesigner has created its own which is stored in its own way. In the past GSoC project, CellDesigner plug­in that enables to export SBML Layout. To further expand from this software, I will implement a standalone software that converts CellDesigner annotation to SBML Layout and vice versa. It will allow the user to convert CellDesigner annotation into SBML format without CellDesigner. Also the same layout will be held in CellDesigner even when a model is created with another software (i.e. SBML model with Layout). From above, implementing this software will provide interconvertibility between CellDesigner and SBML Layout and remove redundancy for users.




  • Akira Funahashi