1. TinkerCell will come with a folder full of modules, e.g. enzyme kinetics, gene regulation
2. Each reaction arc, such as a gene regulation arc, can be used to represent one of these modules. The interface will allow the user to double click on the gene regulation connector and load one of the modules to represent that process.
3. All modules will be encapsulated by default. Input/outputs will be represented using small input/output indicators on the items inside the module.
4. Users will be able to write Octave code for TinkerCell.