2.1         Switching to the Biopathway Modeling Mode

The menu command View | Gene Net Mode switches between the biopathway modeling and gene network modes. If this menu item is checked then you are in the Gene Net mode, otherwise you are in the Biopathway modeling mode.

Any model that has been opened in the CI workspace (or imported) can be viewed in each of both CI modes: Biopathway Modeling and Gene Network mode. However there are the following limitations:

·        Do not view large gene networks in the Biopathway Modeling mode

Displaying large networks with hundreds of edges in the biopathway modeling mode will cause performance problems. Therefore they should be displayed in the Gene Network mode only.

·        A typical gene network cannot be simulated.

Originally a gene network does not contain any data useful for the simulation. After switching to the Biopathway Modeling mode you will see that all simulation parameters for a gene network have default values. Simulating such a net will not give any reasonable results. However such a net can be used as the starting point for creating a simulatable model.

·        A biopathway model might not be a correct gene network model

This is the case if one process has more than one input or output entities, which is normal for Petri net models of biopathways, but forbidden for gene networks. In the case of such a conflict some connection between entities will be ignored. In the gene network view one process is represented by one edge connecting the input and output entity of this process. For each process with multiple input or output entities, the edge connects only one input and output entity of the process.