Difference between revisions of "Tutorial on the basic interaction function"

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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, [[Full freshly minted interaction function| here is a full freshly minted interaction function]]. [[Tutorial on the interaction function details|It is discussed in more detail here.]])<br><br>
 
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, [[Full freshly minted interaction function| here is a full freshly minted interaction function]]. [[Tutorial on the interaction function details|It is discussed in more detail here.]])<br><br>
 
<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>
 
<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>
The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our source code control,
+
The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to  
lines starting with % are comments</span>
+
our source code control, lines starting with % are comments</span>
  
    function m = gpt_why_matlab_2011_05_05( m )
+
<span style="color: CornflowerBlue">Section 1 '''This part is generated automatically''' from the GUI
    %m = gpt_why_matlab_2011_05_05( m )
+
The name matches the project name (the project name is forced into lowercase), GFtbox revision number refers to our
    %   Morphogen interaction function.
+
source code control, lines starting with % are comments</span>
    %   Written at 2011-05-28 08:08:11.
+
    function m = gpt_why_matlab_2011_05_05( m )
    GFtbox revision 3544, 2011-05-25 13:37:23.907904.
+
    <span style="color: Green">%m = gpt_why_matlab_2011_05_05( m )</span>
    % The user may edit any part of this function between delimiters
+
    <span style="color: Green">%  Morphogen interaction function.</span>
    % of the form "USER CODE..." and "END OF USER CODE...".  The
+
    <span style="color: Green">Written at 2011-05-28 08:08:11.</span>
    % delimiters themselves must not be moved, edited, deleted, or added.
+
    <span style="color: Green">%   GFtbox revision 3544, 2011-05-25 13:37:23.907904.</span>
        if isempty(m), return; end
+
        fprintf( 1, '%s found in %s\n', mfilename(), which(mfilename()) );
+
    <span style="color: Green">% The user may edit any part of this function between delimiters</span>
        try
+
    <span style="color: Green">% of the form "USER CODE..." and "END OF USER CODE...".  The</span>
            m = local_setproperties( m );
+
    <span style="color: Green">% delimiters themselves must not be moved, edited, deleted, or added.</span>
        catch
+
        end
+
        if isempty(m), return; end
        realtime = m.globalDynamicProps.currenttime;
+
    %%% USER CODE: INITIALISATION
+
        fprintf( 1, '<span style="color: Green">%s found in %s\n', mfilename(), which(mfilename()) );</span>
<span style="color: CornflowerBlue">'''This part could contain user code'''<br>
+
but in this case there is nothing we need to do before the system extracts  
+
        try
information from the '''Mesh''' data structure</span>
+
            m = local_setproperties( m );
  User code
+
        catch
<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>
+
        end
Variables are extracted from Mesh and the mesh itself is summarised in a set of comments</span>
+
    %%% END OF USER CODE: INITIALISATION
+
        realtime = m.globalDynamicProps.currenttime;
    %%% SECTION 1: ACCESSING MORPHOGENS AND TIME.
+
    %%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.
+
    <span style="color: Green">%%% USER CODE: INITIALISATION</span>
        if isempty(m), return; end
+
<span style="color: CornflowerBlue">Section 2 This part could contain user code
        setGlobals();
+
but in this case there is nothing we need to do before the system extracts information from the Mesh data structure</span>
        global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER
+
   
        global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST
+
    <span style="color: Green">%%% END OF USER CODE: INITIALISATION</span>
        dt = m.globalProps.timestep;
+
        polariser_i = gNEW_POLARISER;
+
<span style="color: CornflowerBlue">Section 3 This part is generated automatically from the GUI
        P = m.morphogens(:,polariser_i);
+
Variables are extracted from Mesh and the mesh itself is summarised in a set of comments</span>
        [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' );
+
    <span style="color: Green">%%% SECTION 1: ACCESSING MORPHOGENS AND TIME.</span>
        [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' );
+
    <span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>
        [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' );
+
        [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' );
+
        if isempty(m), return; end
        [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' );
+
        [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' );
+
        setGlobals();
        [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' );
+
        global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER
        [id_a_i,id_a_p,id_a_a,id_a_l] = getMgenLevels( m, 'ID_A' );
+
        global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST
        [id_b_i,id_b_p,id_b_a,id_b_l] = getMgenLevels( m, 'ID_B' );
+
        dt = m.globalProps.timestep;
    % Mesh type: circle
+
        polariser_i = gNEW_POLARISER;
    %          centre: 0
+
        P = m.morphogens(:,polariser_i);
    %      circumpts: 48
+
        [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' );
    %      coneangle: 0
+
        [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' );
    %        dealign: 0
+
        [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' );
    %          height: 0
+
        [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' );
    %        innerpts: 0
+
        [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' );
    %     randomness: 0.1
+
        [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' );
    %          rings: 6
+
        [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' );
    %        version: 1
+
        [id_a_i,id_a_p,id_a_a,id_a_l] = getMgenLevels( m, 'ID_A' );
    %          xwidth: 0.2
+
        [id_b_i,id_b_p,id_b_a,id_b_l] = getMgenLevels( m, 'ID_B' );
    %          ywidth: 0.2
+
    %            Morphogen  Diffusion  Decay  Dilution  Mutant
+
    <span style="color: Green">% Mesh type: circle</span>
    %            -------------------------------------------------
+
    <span style="color: Green">%          centre: 0</span>
    %                KAPAR        ----    ----      ----    ----
+
    <span style="color: Green">%      circumpts: 48</span>
    %                KAPER        ----    ----      ----    ----
+
    <span style="color: Green">%      coneangle: 0</span>
    %                KBPAR        ----    ----      ----    ----
+
    <span style="color: Green">%        dealign: 0</span>
    %                KBPER        ----    ----      ----    ----
+
    <span style="color: Green">%          height: 0</span>
    %                KNOR        ----    ----      ----    ----
+
    <span style="color: Green">%        innerpts: 0</span>
    %            POLARISER        ----    ----      ----    ----
+
    <span style="color: Green">%     randomness: 0.1</span>
    %            STRAINRET        ----    ----      ----    ----
+
    <span style="color: Green">%          rings: 6</span>
    %              ARREST        ----    ----      ----    ----
+
    <span style="color: Green">%        version: 1</span>
    %                ID_A        ----    ----      ----    ----
+
    <span style="color: Green">%          xwidth: 0.2</span>
    %                ID_B        ----    ----      ----    ----
+
    <span style="color: Green">%          ywidth: 0.2</span>
    %%% USER CODE: MORPHOGEN INTERACTIONS
+
<span style="color: CornflowerBlue">'''This part contains user code that articulates the model'''
+
    <span style="color: Green">%            Morphogen  Diffusion  Decay  Dilution  Mutant</span>
</span>
+
    <span style="color: Green">%            -------------------------------------------------</span>
        if (Steps(m)==0) && m.globalDynamicProps.doinit  % Initialisation code.
+
    <span style="color: Green">%                KAPAR        ----    ----      ----    ----</span>
            id_a_p(m.nodes(:,1)<-0.03)=1; % setup region for A
+
    <span style="color: Green">%                KAPER        ----    ----      ----    ----</span>
            id_b_p(m.nodes(:,2)<-0.01)=1; % setup region for B
+
    <span style="color: Green">%                KBPAR        ----    ----      ----    ----</span>
        else
+
    <span style="color: Green">%                KBPER        ----    ----      ----    ----</span>
            % @@KRN Growth Regulatory Network
+
    <span style="color: Green">%                KNOR        ----    ----      ----    ----</span>
            kapar_p(:) = id_a_l .* inh(1,id_b_l); % growth rate
+
    <span style="color: Green">%            POLARISER        ----    ----      ----    ----</span>
            kaper_p(:) = kapar_p; % isotropic growth
+
    <span style="color: Green">%            STRAINRET        ----    ----      ----    ----</span>
            kbpar_p(:) = kapar_p; % same on both sides of the sheet
+
    <span style="color: Green">%              ARREST        ----    ----      ----    ----</span>
            kbper_p(:) = kapar_p; % same
+
    <span style="color: Green">%                ID_A        ----    ----      ----    ----</span>
            knor_p(:)  = 0;      % thickness not growing
+
    <span style="color: Green">%                ID_B        ----    ----      ----    ----</span>
        end
+
<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br>
+
<span style="color: CornflowerBlue">Section 4 This part contains user code that articulates the model</span>
Variables are put back into the data structure (Mesh).<br>
+
     
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.</span>
+
    <span style="color: Green">%%% USER CODE: MORPHOGEN INTERACTIONS</span>
    %%% END OF USER CODE: MORPHOGEN INTERACTIONS
+
        if (Steps(m)==0) && m.globalDynamicProps.doinit  <span style="color: Green">% Initialisation code.</span>
    %%% SECTION 3: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE
+
            id_a_p(m.nodes(:,1)<-0.03)=1; <span style="color: Green">% setup region for A</span>
    %%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.
+
            id_b_p(m.nodes(:,2)<-0.01)=1; <span style="color: Green">% setup region for B</span>
        m.morphogens(:,polariser_i) = P;
+
        else
        m.morphogens(:,kapar_i) = kapar_p;
+
            <span style="color: Green">% @@KRN Growth Regulatory Network</span>
        m.morphogens(:,kaper_i) = kaper_p;
+
            kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>
        m.morphogens(:,kbpar_i) = kbpar_p;
+
            kaper_p(:) = kapar_p; <span style="color: Green">% isotropic growth</span>
        m.morphogens(:,kbper_i) = kbper_p;
+
            kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>
        m.morphogens(:,knor_i) = knor_p;
+
            kbper_p(:) = kapar_p; <span style="color: Green">% same</span>
        m.morphogens(:,strainret_i) = strainret_p;
+
            knor_p(:)  = 0;      <span style="color: Green">% thickness not growing</span>
        m.morphogens(:,arrest_i) = arrest_p;
+
        end
        m.morphogens(:,id_a_i) = id_a_p;
+
<span style="color: CornflowerBlue">Section 5 This part is generated automatically from the GUI
        m.morphogens(:,id_b_i) = id_b_p;
+
Variables are put back into the data structure (Mesh).
    %%% USER CODE: FINALISATION
+
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.</span>
<span style="color: CornflowerBlue">'''This part could contain user code'''<br>
+
    <span style="color: Green">%%% END OF USER CODE: MORPHOGEN INTERACTIONS</span>
that manipulates the data structure</span>
+
  User code
+
    <span style="color: Green">%%% SECTION 6: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE</span>
<span style="color: CornflowerBlue">'''This part is generated automatically from the GUI'''<br></span>
+
    <span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>
    %%% END OF USER CODE: FINALISATION
+
        m.morphogens(:,polariser_i) = P;
    end
+
        m.morphogens(:,kapar_i) = kapar_p;
    %%% USER CODE: SUBFUNCTIONS
+
        m.morphogens(:,kaper_i) = kaper_p;
<span style="color: CornflowerBlue">'''This part could contain user code'''<br>
+
        m.morphogens(:,kbpar_i) = kbpar_p;
add any local functions that might be need<br><br>
+
        m.morphogens(:,kbper_i) = kbper_p;
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</span>
+
        m.morphogens(:,knor_i) = knor_p;
    function m = local_setproperties( m )
+
        m.morphogens(:,strainret_i) = strainret_p;
    end
+
        m.morphogens(:,arrest_i) = arrest_p;
 +
        m.morphogens(:,id_a_i) = id_a_p;
 +
        m.morphogens(:,id_b_i) = id_b_p;
 +
 +
    <span style="color: Green">%%% USER CODE: FINALISATION</span>
 +
 +
    <span style="color: Green">%%% END OF USER CODE: FINALISATION</span>
 +
   
 +
    end
 +
 +
 +
    <span style="color: Green">%%% USER CODE: SUBFUNCTIONS</span>
 +
 +
<span style="color: CornflowerBlue">Section 5</span>
 +
    function m = local_setproperties( m )
 +
    end

Revision as of 12:28, 31 May 2011

Back to tutorial pages

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)

GFtbox interface

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
Section 1 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
Section 2 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

    %%% END OF USER CODE: INITIALISATION

Section 3 This part is generated automatically from the GUI
Variables are extracted from Mesh and the mesh itself is summarised in a set of comments
    %%% 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        ----    ----       ----     ----

Section 4 This part contains user code that articulates the model
     
    %%% USER CODE: MORPHOGEN INTERACTIONS
        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
Section 5 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 6: 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

    %%% END OF USER CODE: FINALISATION

    end


    %%% USER CODE: SUBFUNCTIONS

Section 5
    function m = local_setproperties( m )
    end