STI-GMaS Main Window

On launching STI-GMaS, the user is presented with the STI-GMaS 'Main Window', from which the user can select from a list of models included. Models are categorised as either temporal or spatio-temporal; each category has a corresponding 'More Information' button (see below), which will provide further information as to the modelling strategies associated with each model, further informing the user as to which style of model is most appropriate to their studies. On selecting a model, the main window is replaced by a model specific control panel, from which simulations can be run.

User Guide

Model Simulation Windows

Having selected a model, the user will be presented with a window similar to that shown below. The window contains the following key features:

  • Model code - an identifier unique to each model.

  • Model citation.

  • Description of the model, including biological phenomena incorporated, associated parameters etc.

  • A list of all the model's parameters, displayed with default values and units (where appropriate).

  • 'Run Simulation' button, which will simulate the model with the chosen parameters, and launch the appropriate software to visaulise the results.

Menus:

  • File menu:

    • Close - return to STI-GMaS main window to select an alternative model.

    • Quit - exit STI-GMaS completely.

  • ParameterSets menu:

    • Save ParameterSet - save the current parameter set to file for future use.

    • Load ParameterSet - load a previously saved parameter set for new simulation.

  • Help menu:

    • Help - link to online documentation.

    • About - displays version information.

 

Parameters are always presented with nomenclature consistent with the original publication. Hovering the mouse pointer over the name of any parameter will display information as to what that parameter represents. The user can set parameter values either by typing directly into the appropriate text boxes, or by loading a complete parameter set through the ParameterSets menu. Once parameters are set, the user can select 'Run Simulation', which will execute the appropriate CHASTE codes to simulate the model with the given parameters, and then launch the appropriate software for visualising the results (Gnuplot for temporal models, Paraview for spatio-temporal models).

Paraview (for 2D spatio-temporal models)

 

1. When STI-GMaS launches paraview, the most recent model simulation results are loaded automatically. On some systems, the user will need to select "Apply" (found in the 'Properties' panel of the Object Inspector tab) on the pre-loaded data-set in order to make paraview display the results. See screenshot below. Note: This can be automated for future sessions by navigating to "Settings" within the "Edit" menu, and checking the "Auto Accept" box.

2. Next, the user should select the 'Display' tab of the Object Inspector, and in the 'Color by' drop-down list, select the results of interest. In the Mallet2009 model, for example, the data is named "Extracellular Chlamydia".

 

3. The user can select the colorbar button on the toolbar to display the colour scale as shown.

 

4. By default, paraview will select a linear color scale based upon the minimum and maximum values of the loaded data. It can sometimes be helpful to modify this, rescaling on a given timestep's data via the 'Rescale to data range' button. For more accurate control of coloring, the user can select 'Edit color map', but this requires more lengthy specification, which is often not required.

 

5. An animation of the results can be started and controlled by the buttons illustrated below.