5.2 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 BiologicalNetworks 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 BiologicalNetworks.

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

5.2.1 Saving Models

Models constructed in BiologicalNetworks 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 .bnm format, which is essentially a binary format of the model Java class.
The .bnm 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.

5.2.2 Importing Models

BiologicalNetworks can import models created in the .bnm (BiologicalNetworks) format or a model specified in the SBML format.

BiologicalNetworks 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 .bnm 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 .bnm file. SBML does not specify information for the layout of the network on the model workspace. BiologicalNetworks uses an intelligent layout algorithm for automatically creation of network layout from the SBML information.

5.2.3 Exporting Models

BiologicalNetworks 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.