Global parameters in the Virtual Cell are defined at the physiology or Model level. They can be numeric constants or functions with other global parameters or species concentrations. They can be used in reaction rate expressions or other local parameter expressions in reactions.

Creating a global parameter:

To create a new global parameter, select any compartment in the model and using the right mouse button, select the ‘Add Global Parameter’ menu item to open the “Add Global Parameters” dialog where the name, expression, units and annotations for the new global parameter can be provided (Fig. 1).

Fig. 1

Viewing global parameters:

There are two ways to view global parameters.

1. Select any compartment in the model and using the right mouse button, select the ‘Parameters and Rate Expressions’ menu item. This opens a table of all parameters in the model which includes global parameters, all reaction rates and their local parameters (Fig. 1).

2. Within the Kinetic Reaction Editor, a button is provided that will generate a list of all global parameters (Fig. 2].

Fig. 2

Editing global parameters:

In the Parameters and Rate Expressions Panel, double click on the name, expression, unit and annotation cells of global parameters to edit the respective field.

Options available to user from this panel using the right mouse button on the parameters table:

• Add global parameter

• Delete global parameter

• ‘Merge to Single Global Parameter’ allows user to select a few local reaction kinetic parameters and promote them to a single global parameter (useful where user has same local parameter defined in multiple reactions that can be replaced by a single global)

• ‘Convert to Local Parameter’ allows user to ‘push-down’ a global parameter to the reactions where it is referenced.

Conversion of local to global parameter and vice versa:

Parameters can be converted from local to global and vice versa in the Parameters and Rate Expressions Panel or the Reaction Kinetics Editor. The column ‘Global’ in Reaction Kinetics Editor has a checkbox that is enabled for global parameters and user-defined local parameters in the kinetics. Checking or un-checking the box converts the parameter from local to global or vice versa.