Ready Reference Manual

Summary of controls

Roll the mouse over any control and information about the control will pop-up.

Outputs

Plotting panel

To view

• Specified values, i.e. kapar or a particular morphogen (factor) select from drop down menu top right and tick Plot current factor
• Output variables, e.g. growth rate, tick Plot output value and make selection from the two drop down menus.
• Plotting problems means that it is a good idea to tick/untick Monochrome control.
• thickness, tick/untick Menu:Plot:Thickness

To show/hide

• thickness, tick/untick Menu:Plot:Thickness
• mesh, tick/untick FE edges
• axes, tick/untick Menu:Plot:Show/Hide axes
  
• legend, tick/untick Menu:Plot:Show/Hide legend - also Set legend to choose heading
  

To set/modify values of morphogens (best done in the interaction function)

• Choose morphogen (list box), Click on Select Tool:Factors, '---' list box to select action and click on appropriate button (Add constant or Add radial, etc).
• at individual nodes (vertices). Choose morphogen (list box), Click on Select Tool:Factors, '---' list box to select action and click on node.
  

To clip the mesh (hide part of the mesh)

• Tick Clipping plane and choose the plane with Az (azimuth), ti (tilt), D
• Tick Clip and select the region to hide by using morphogen values (click on Mgens button)

Snapshots

Saved in png format in the project snapshots subdirectory

• Clicking Take snapshot makes a png file copy of the plotting screen. At the same time a copy of the interaction function (relabelled to have .txt as a suffix) is also made - to help document the snapshot.
• Publication quality screenshot is made by changing the action of the Snapshot button using Menu:Misc:Hi-res snapshots and choosing a number of dots per inch.

VRML, OBJ, FIG

To export the current mesh

• VRML, to interactively view the mesh using a web browser export the mesh as a VRML file, Menu:Mesh:Save VRML. We use such files to make 3D prints.
• FIG, for Matlab figure files.

Movies

By default movies are uncompressed and stored in the projects movies subdirectory

• To compress select Menu:Movie:Codec - we currently favour Motion JPEG avi
• To automatically convert the output to flash, .flv, select Menu:Movie:Convert to flash. This option requires the ffmpeg program to be on the current path.
• Click Record Movie to start creating a movie. The button will change to Stop Movie.

Useful programming constructs

The patterns of morphogens A and B are set up by

       id_a_p(m.nodes(:,1)<-0.03)=1; 
       id_b_p(m.nodes(:,2)<-0.01)=1; 

where id_a_p is the A morphogen. m.node(:,1) refers to the x coordinates of all nodes (vertices) in the mesh
The expression (m.nodes(:,1)<-0.03) means find all vertices with x coordinates that are less than -0.03.

Similarly, (m.nodes(:,2)<-0.01) means find all vertices with y coordinates that are less than -0.01.

And the pattern of polariser (P) is set up by

       P((m.nodes(:,1)<-0.05)&(m.nodes(:,2)>0.03))=1;

Where (m.nodes(:,1)<-0.05)&(m.nodes(:,2)>0.03) means find all vertices with x,y coordinates that are less than -0.05 and greater than 0.03 respectively

Thus the full code describing the model is:

   if (Steps(m)==0) && m.globalDynamicProps.doinit  % Initialisation code.
       id_a_p(m.nodes(:,1)<-0.03)=1; % setup region for A where identity factor A is represented by id_a_p
       id_b_p(m.nodes(:,2)<-0.01)=1; % setup region for B
   else
       % @@KRN Growth Regulatory Network
       kapar_p(:) = id_a_l .* inh(1,id_b_l); % growth rate
       kaper_p(:) = kapar_p; % isotropic growth
       kbpar_p(:) = kapar_p; % same on both sides of the sheet
       kbper_p(:) = kapar_p; % same
       knor_p(:)  = 0;       % thickness not growing
   end