In the beginning Uniform

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We start with a number of very large screenshots (they are just here to orient you). They show the GFtbox graphical interface.

Modelling uniform growth using the GUI alone

First view

At first view the interface is daunting but try not to dispair. Some people, us at least, think it has a logic. It is divided into a set of panels. The largest is the plotting window on the right. Just to the left is a column of buttons, tick boxes, drop-down lists and buttons that control the plotting window.

Top left is a panel for loading and saving projects. (one of the most used is Reset. If you have made a programming mistake in the interaction function it is necessary to Reset the GUI).

Below this is a Panel for selecting tools. These buttons select what Panel will be visible below, e.g. Mesh Editor, or Factors (for adding morphogens), etc.

At the bottom left are controls for running the model: Step, run for a specified number of steps, for a specified (model) time, run to a certain area (e.g. 2 times starting area). Above the Run Panel is a Panel for electing to Edit the interaction function, call the interaction function without actually growing.

There are also controls on the Menu bar. At this stage you might consider that the GUI has the wrong sized font. It can be changed through the Menu:Misc:GUI format control.

The GFtbox user interface. Focus on the Select Tool Panel. Here the Mesh Editor has been selected and the Mesh Editor panel is visible. Idea: change all GFtbox font sizes using Menu Misc:Gui Format

Add a mesh (canvas that represents tissue)

Create a canvas by clicking on Panel Mesh Editor:new. A variety of preset shapes are available, here we choose a Circle with 4 concentric rings of nodes that is 2 mm in diameter. By default the mesh is autoscaled and autocentred - it makes it easier to see shape changes but to see growth these are best turned off. Set the Panel:Plot options:Auto axis range to unticked and insert plot ranges -2.5 to 2.5 on x and y axes and 0 0 on z. Also turn off Menu:Plot:Autozoom and centre. Idea: Special shapes can be imported as OBJ files.

Add a pattern of growth factor

Select Tool:Factors makes the Morphogen Panel visible. Currently we are controlling the KAPAR factor. It has been selected from a drop down list top right (Plot current factor). We add a constant level of KAPAR. Make sure that the Panel Plot Options:Monochrome is ticked and the gradient of KAPAR will be as shown. Do the same for the top face, KBPAR.

And grow

Now save the project using the Save As button. A dialogue box will open - here we keyed in in_the_beginning and the prefix GPT_ and the suffix _date was added automatically. A directory is created with the project name which contains all the files needed for the project and any results (snapshots, movies) we create. Select Tool:Simulation makes the Simulation Panel visible. Change the Panel Run:Run until box to 2 and click the Panel Run:Run until button. The canvas will grow in steps set by the Panel Simulation:Timescale box. Warning: saving is essential if you want to Restart the simulation or if you want to save a movie. Idea: set the axes manually (here to +-3) and turn off Panel:Plot Options: Auto axis range and Menu:Plot:Auto zoom and centre. This enables growth to be seen as a change of size rather than change of axis range. Idea: take a snapshot of the canvas by pressing Take snap... (c.f. image on right, button is bottom right of GUI controls) Idea: to create an uncompressed movie of your simulation, before running click the Record movie and when it is finished click Stop movie. The movie will be in the Project directory. We normally compress the movies using Microsoft Live Movie Maker or Quicktime.

The canvas is not flat because it started not flat. By default, a new mesh is given a small amount of random noise to allow deformations out of the plane. (This can be suppressed.)