4.3 Managing Models and SBML Support

Building models of biological processes, is an intensive and tedious exercise. As a result re-usability and ease of exchange of models is an asset for any software tool aimed at studying biological networks and processes.

In Cellware this requirement has been addressed by making it compliant with the SBML standard (www.sbml.org). SBML is an XML based modelling language for describing biochemical network models. It is an ongoing international collaboration effort and is fast becoming a standard for biochemical model specification and exchange. The current release versions of SBML (Level 1 version 1, Level 2 version 1, Level 2 version 2) are supported by Cellware.

Following sections describe how to save, import and export models in Cellware.

4.3.1 Saving Models

Models constructed in Cellware can be saved by using the save option in the menu or through the save icon in the toolbar. The models are saved in the proprietary .cwm format, which is essentially a binary format of the model Java class.
The .cwm file captures all the network information entered through species editor, reaction editor, simulation setup window and the layout of the network on the model workspace.

4.3.2 Importing Models

Cellware can import models created in the .cwm (cellware) format or a model specified in the SBML format.

Cellware models can be imported by simply choosing the open option from the File menu or by clicking on the open icon in the toolbar and then browsing for the .cwm file. The model would be created along with the network layout.

SBML models can be imported by using the Import SBML option from the File menu and then browsing for the .cwm file. SBML does not specify information for the layout of the network on the model workspace. Cellware uses an intelligent layout algorithm for automatically creation of network layout from the SBML information.

4.3.3 Exporting Models

Cellware models can be exported to SBML file. User can use the Export SBML option from the File menu and then specify the file name and the version of SBML to exported the model. However, certain information for example the simulation setup and layout information will not be saved in the SBML files.