Tutorial on the basic interaction function
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 |
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| suffixes | _p, _l, _a, _i |
Full details of types of morphogens and factors
| Pre-defined variables |
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| Pre-defined functions |
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The interaction function in more detail
This part is generated automatically from the GUI
The name matches the project name, 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) that are stored (levels _l can be computed on the fly and activities are generally set in the GUI - in the interaction function they would have to be changed directly in the data structure.
%%% 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