Systems Biology plugin
This plugin will provide support for systems biology. The inital release will encompass support for SBML and basic simulation of these networks.
A custom SBML parser will be implemented to avoid relying on native libraries.
The editor will become a multi page editor. For its initial version it will encompass an XML editor, and an Outline. Once the things have been settled, a graphical editor based upon GEF is planed.
The simulation part will constit of ODEs. Stochastic and hybrid methods are considered in later versions.
- Project has been setup and bc_sysbio has been created within the Bioclipse SVN.
- A new BioResource derived SBMLResource has been created.
- (5th) A prototype of the SBML parser supporting a minimal subset of the specification (as needed for further prototypes) has been implemented.
- (5th) Work for the simulation prototype has been just started. Initial code was commited.
- (7th) Work on the Simulation View has begun. This provides the results of the simulation by tabular or graphical representation.
- (11th) Work on the Form Editor has begun.