Parameters and Functions

Users can define parameters to aid in modeling their virtual experiments or applications. User-defined parameters can be added at the physiology level either as global parameters or as reaction parameters. There are other predefined parameters such as species initial conditions, structure sizes or reaction rates for the different kinetic types that are generated as the model is being developed, for which the user has to provide values. The parameter values can be numeric or expressions involving other allowable variables in the model. Parameter values that are expressions are referred to as Functions in the Virtual Cell.

Viewing/Editing Parameters and Functions

• Activate by clicking the Parameters, Functions and Units item from the tree list in the Navigation panel (window upper left) which will display the 'Parameters and Functions' tab (window right panel).
• View by clicking the Parameters and Functions tab. A table of information including 'Defined In' (where the parameter/function is defined), Name, Description (type of parameter/function), Expression (value of parameter/function), Units. Defined In can be 'Global', 'Model/Reaction' (created in reactions add/edit) and 'App' (varies in application, e.g. initial conditions, compartment size, diffusion, boundary condition, etc... See application specifications).
• Filter displayed items by clicking any of the 'Defined In:' check-boxes. 'Global' displays global model parameters that were created with the 'New global Parameter' button. 'Reactions and Rules' displays reactions and any parameters and constants defined within reactions and rules. 'Applications' displays application related items such as diffusion, initial concentration, boundary condition, etc... The 'Type:' check-boxes further restrict the display to 'parameters' (named numerical values) or 'functions' (expressions that may contain parameters). ''
• Search table rows by entering text in the Search text-box. The table will be updated to display only rows that have matching text in one or more of the columns.
• Edit Parameter/Function a parameter or function by selecting a row from the displayed table. Detailed information about the selected parameter/function will appear in the 'Object Properties' tab below the table. The information includes Name, Description, Unit, Expression, Annotation. One or more of the displayed detail items are editable depending on the parameter/function type. 'Expression' and 'Unit' can also be edited by double-clicking in the table cell or by activating the mouse pop-up menu within a table cell. See also Parameters Properties Pane.
• Add Global Parameter by clicking the New Global Parameter button. The new parameter will appear in the table as a 'Global Parameter' that can be used in expressions in all applications in the BioModel.
• Delete Global Parameter (column Description 'Global Parameter') by selecting one or more table rows and pressing the Delete global Parameter(s) button. If the 'Global Parameter' is used in an expression anywhere in the VCell model a warning dialog will be displayed and the parameter will not be deleted.