Tutorial on the basic interaction function

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Creating the interaction function from the GUI

The GFtbox user interface. Having saved a new project, click on Panel: Interaction function: Edit (bottom left) and the initial interaction function will be generated automatically. A free-text file with the same name as the interaction function is also created automatically on pressing Panel:Interaction function: notes. This makes it easier to keep notes on what you are doing. Note: you can see the internal data structure by clicking Menu: Wizard: Export mesh and follow the instructions shown at the command line. Another way to see Mesh m is to set a break point in the interaction function and running (e.g. Panel: Run: Step, or Panel: Interaction function: Call, etc.) Note: a history of commands that have been run recently can be displayed (can be used to help write custom modelling programs that exploit the GFtbox library)

Variables and utility functions

Variables that need to be seen in the GUI (morphogens, growth factors, signals, etc.) are always set up (declared) from the GUI using Morphogen Panel. We have evolved a naming convention

prefixes	id_ identity factor s_ signalling factor v_ visual monitor f_ finite element monitor
suffixes	_p, _l, _a, _i

Full details of types of morphogens and factors

Pre-defined variables	dt computational step size realtime virtual time of the model
Pre-defined functions	Steps(m) current step number in Mesh m pro(k,id) promote by k in regions designated by factor, id inh(k,id) inhibit by k in regions designated by factor, id local_setproperties( m ) initialise Mesh properties leaf_*( m, *) A large library of functions for manipulating the Mesh data structure, m. Many are listed in the GUI help system, Menu:Help

The interaction function in more detail

A large number of comments have been deleted to allow us to focus on the essential components. (What are these deleted comments? They provide hints and clues on how to program a model - many people use the system and we found the easiest way for people to remember how to program models is to provide comments in the appropriate place - which can be deleted when not needed. Ok so you want see an uncensored version, here is a full freshly minted interaction function. It is discussed in more detail here.)

This part is generated automatically from the GUI
The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our source code control, lines starting with % are comments

   function m = gpt_why_matlab_2011_05_05( m )
   %m = gpt_why_matlab_2011_05_05( m )
   %   Morphogen interaction function.
   %   Written at 2011-05-28 08:08:11.
   %   GFtbox revision 3544, 2011-05-25 13:37:23.907904.
   % The user may edit any part of this function between delimiters
   % of the form "USER CODE..." and "END OF USER CODE...".  The
   % delimiters themselves must not be moved, edited, deleted, or added.
       if isempty(m), return; end
       fprintf( 1, '%s found in %s\n', mfilename(), which(mfilename()) );
       try
           m = local_setproperties( m );
       catch
       end
       realtime = m.globalDynamicProps.currenttime;
   %%% USER CODE: INITIALISATION

This part could contain user code
but in this case there is nothing we need to do before the system extracts information from the Mesh data structure

User code

This part is generated automatically from the GUI
Variables are extracted from Mesh and the mesh itself is summarised in a set of comments

   %%% END OF USER CODE: INITIALISATION
   %%% SECTION 1: ACCESSING MORPHOGENS AND TIME.
   %%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.
       if isempty(m), return; end
       setGlobals();
       global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER
       global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST
       dt = m.globalProps.timestep;
       polariser_i = gNEW_POLARISER;
       P = m.morphogens(:,polariser_i);
       [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' );
       [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' );
       [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' );
       [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' );
       [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' );
       [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' );
       [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' );
       [id_a_i,id_a_p,id_a_a,id_a_l] = getMgenLevels( m, 'ID_A' );
       [id_b_i,id_b_p,id_b_a,id_b_l] = getMgenLevels( m, 'ID_B' );
   % Mesh type: circle
   %          centre: 0
   %       circumpts: 48
   %       coneangle: 0
   %         dealign: 0
   %          height: 0
   %        innerpts: 0
   %      randomness: 0.1
   %           rings: 6
   %         version: 1
   %          xwidth: 0.2
   %          ywidth: 0.2
   %            Morphogen   Diffusion   Decay   Dilution   Mutant
   %            -------------------------------------------------
   %                KAPAR        ----    ----       ----     ----
   %                KAPER        ----    ----       ----     ----
   %                KBPAR        ----    ----       ----     ----
   %                KBPER        ----    ----       ----     ----
   %                 KNOR        ----    ----       ----     ----
   %            POLARISER        ----    ----       ----     ----
   %            STRAINRET        ----    ----       ----     ----
   %               ARREST        ----    ----       ----     ----
   %                 ID_A        ----    ----       ----     ----
   %                 ID_B        ----    ----       ----     ----
   %%% USER CODE: MORPHOGEN INTERACTIONS

This part contains user code that articulates the model

       if (Steps(m)==0) && m.globalDynamicProps.doinit  % Initialisation code.
           id_a_p(m.nodes(:,1)<-0.03)=1; % setup region for A
           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

This part is generated automatically from the GUI
Variables are put back into the data structure (Mesh).
Note: only variables with the _p suffix (promotors) are stored (levels _l can be computed on the fly and activities _a are generally set in the GUI - they can only be changed in the interaction function by altering the data structure itself.

   %%% END OF USER CODE: MORPHOGEN INTERACTIONS
   %%% SECTION 3: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE
   %%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.
       m.morphogens(:,polariser_i) = P;
       m.morphogens(:,kapar_i) = kapar_p;
       m.morphogens(:,kaper_i) = kaper_p;
       m.morphogens(:,kbpar_i) = kbpar_p;
       m.morphogens(:,kbper_i) = kbper_p;
       m.morphogens(:,knor_i) = knor_p;
       m.morphogens(:,strainret_i) = strainret_p;
       m.morphogens(:,arrest_i) = arrest_p;
       m.morphogens(:,id_a_i) = id_a_p;
       m.morphogens(:,id_b_i) = id_b_p;
   %%% USER CODE: FINALISATION

This part could contain user code
that manipulates the data structure

User code

This part is generated automatically from the GUI

   %%% END OF USER CODE: FINALISATION
   end
   %%% USER CODE: SUBFUNCTIONS

This part could contain user code
add any local functions that might be need

The following function is always created. It is automatically filled with comments (here deleted) when the project is first created. It will be discussed later

   function m = local_setproperties( m )
   end