Top Menu and Button Bar

We describe the functionality of the button bar and the top menu. In many cases the options are only placeholders for functionality to be added later. We will update this document as these options are implemented.

Menu Bar

File Menu

The file menu contains items generally related to loading/creating/saving files. The options are:

New Model

Creates a new session.

Save

Save the session in the currently selected tab.

Import SBML

Import a file saved in the SBML format and create a new DEDiscover session based on the model described.

Exit

Exit from DEDiscover.

Edit Menu

The edit menu will eventually allow editing of the equations, but is not currently implemented.

Model Lib Menu

Not yet implemented but will contain all the sessions from the session tree.

Data Menu

Contains functionality for the data tab of the current session. The options are:

Import

Import new data into the datatable.

Export

Export the data currently in the datatable in a CSV format.

Clear Data

Remove all the data from the datatable.

Clear Mappings

Remove all the mappings from the middle section of the Data tab.

Run Menu

Actions related to building models and performing computation. The options are:

Parse

Build the model in the model tab, reporting errors if any.

Simulate

Perform the simulation based to the parameters in the Sim:Methods and Sim:Result tabs.

Estimate

Perform the estimation based of the parameters in the Est:Parameters and Est:Methods tabs.

Export Menu

Export various results from the current sessions into files that can be save by the user. It can export plots, some results in CSV format, as well as JSON files that contains the parameters used to generate the results. The options are:

Simulation Results

Export the simulation results from one parameter set. The exported format can be either a tabular (csv) file containing the data at each timestep, or a JSON file containing the simulation results as well as the values of all the control parameters used in the simulation.

Estimation Results

Export the estimation results from from the last estimations. Two files can be exported. A tabular file with the estimated values and some Confidence Interval statistics, and a JSON containing the control parameters used for the estimation.

Plots

Export the plots from the Plots tab into either JPG or PNG files.

Window and Help Menus

Not implemented yet.

Button Bar

There are currently 4 buttons in the bar under the menu bar. They are, going from left to right:

The + button

Will add a new session.

The Floppy Disk button

Will save the current session.

The Round Arrow button

Will reload the current session, not currently implemented.

The Thrash Can button

Will delete the current session.

File Tree Context Menu

Many operations on the session are available by right-clicking on one or many sessions or packages (but not both) in the session tree. Note that some of the operation described below will not be available for built-in sessions.

Available options for packages:

New -> Session

Create a new session that will be located in this package, unless the user specifies a different package later on.

New -> package

Create a new package under this package. It can be more than one package, separated with dots.

Delete

Can apply to multiple package selection. Delete the package(s) and all the contained sessions.

Available options for Sessions:’

Open

Load a session in a new tab.

Duplicate

Make a copy of the selected session.

Delete

Delete the session.

Reload

Reload a session, discarding all changes. (Not yet implemented.)

Rename

Rename a session.