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We illustrate the practical advantage of having submodels within a project and an important con…'

2011-07-01T09:05:30Z

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[[GFtbox Tutorial pages#Output and Results|Back to GFtbox Tutorial pages]] 
We illustrate the practical advantage of having submodels within a project and an important consequence of understanding biological growth within the GPT-framework. 
Conclusion: using a '''combination''' of polarity patterns to set local axes for anisotropic growth and patterns of differential specified growth to regulate the growth of shape would be powerful.
==Illustrating two independent ways to form shapes and the use of submodels. ==
The full interaction function is shown at the bottom. The line of code that selects the submodel and the start of each submodel is shown in red. 
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|'''Uniform specified polariser''' (no polariser gradient). Creating a shape using a specified pattern of isotropic growth. 
'''Result''': simple patterns tend to produce blobby shapes. 
'''Conclusion''': Whilst it may be possible to produce complex shapes such as the outgrowth shown in the GFtbox icon, we don't know how.
|width="180pt"|[[image:GPT TwoWayHeart 20110531-0001 Last.png‎|thumb|180px|Pattern of isotropic specified growth (no polariser)]]
|width="180pt"|[[image:GPT_TwoWayHeart_20110531-0001.png‎|thumb|180px|Pattern of isotropic specified growth after growing to 3 times the original area.]]
|- valign="top"
|width="400pt"|'''Uniform specified growth'''. Creating a shape using a specified pattern of diffusable polariser. 
'''Result''': simple patterns can readily produce sharp shapes. 
'''Conclusion''': It is not so easy to produce blobby shapes using patterns of polariser alone.
|width="180pt"|[[image:GPT_TwoWayHeart_20110531-0002_Last.png‎|thumb|180px|Pattern of specified polariser levels (green-cyan). Polariser can diffuse and the gradient is arrowed. Uniform specified growth (red).]]
|width="180pt"|[[image:GPT_TwoWayHeart_20110531-0002.png‎|thumb|180px|Patterns and shape after growing to 3 times the original area.]]
|- valign="top"
|}
% Section 1
function m = gpt_twowayheart_20110531( m )
%m = gpt_twowayheart_20110531( m )
% Morphogen interaction function.
% Written at 2011-05-31 19:51:32.
% GFtbox revision 3548, 2011-05-31 14:37:10.747930.

% 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;

% Section 2
%%% USER CODE: INITIALISATION

% In this section you may modify the mesh in any way whatsoever.
if (Steps(m)==0) && m.globalDynamicProps.doinit % First iteration
% Set up names for variant models. Useful for running multiple models on a cluster.
m.userdata.ranges.modelname.range = { 'PolariserBased', 'DifferentialGrowthBased' }; % CLUSTER
 m.userdata.ranges.modelname.index = 1; % CLUSTER
end
modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index}; % CLUSTER
disp(sprintf('\nRunning %s model %s\n',mfilename, modelname));

% Set priorities for simultaneous plotting of multiple morphogens, if desired.
m = leaf_mgen_plotpriority( m, {'ID_PLUSORG', 'ID_MINUSORG'}, [1,2], [0.4,0.4] );

% Set colour of polariser gradient arrows.
m = leaf_plotoptions(m,'highgradcolor',[0,0,0],'lowgradcolor',[1,0,0]);
m = leaf_plotoptions(m,'decorscale',1.5);

% setup a multiplot of the following morphogens
m = leaf_plotoptions( m, 'morphogen', {'V_KAREAL','ID_PLUSORG','ID_MINUSORG'});
%%% END OF USER CODE: INITIALISATION

% Section 3
%%% 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_plusorg_i,id_plusorg_p,id_plusorg_a,id_plusorg_l] = getMgenLevels( m, 'ID_PLUSORG' );
[id_minusorg_i,id_minusorg_p,id_minusorg_a,id_minusorg_l] = getMgenLevels( m, 'ID_MINUSORG' );
[v_kareal_i,v_kareal_p,v_kareal_a,v_kareal_l] = getMgenLevels( m, 'V_KAREAL' );
[id_tip_i,id_tip_p,id_tip_a,id_tip_l] = getMgenLevels( m, 'ID_TIP' );
[id_top_i,id_top_p,id_top_a,id_top_l] = getMgenLevels( m, 'ID_TOP' );
[s_growth_i,s_growth_p,s_growth_a,s_growth_l] = getMgenLevels( m, 'S_GROWTH' );
[id_mid_i,id_mid_p,id_mid_a,id_mid_l] = getMgenLevels( m, 'ID_MID' );

% Mesh type: circle
% centre: 0
% circumpts: 24
% coneangle: 0
% dealign: 0
% height: 0
% innerpts: 0
% randomness: 0.1
% rings: 4
% version: 1
% xwidth: 2
% ywidth: 2

% Morphogen Diffusion Decay Dilution Mutant
% -------------------------------------------------
% KAPAR ---- ---- ---- ----
% KAPER ---- ---- ---- ----
% KBPAR ---- ---- ---- ----
% KBPER ---- ---- ---- ----
% KNOR ---- ---- ---- ----
% POLARISER 0.1 ---- ---- ----
% STRAINRET ---- ---- ---- ----
% ARREST ---- ---- ---- ----
% ID_PLUSORG ---- ---- ---- ----
% ID_MINUSORG ---- ---- ---- ----
% V_KAREAL ---- ---- ---- ----
% ID_TIP ---- ---- ---- ----
% ID_TOP ---- ---- ---- ----
% S_GROWTH 0.01 ---- ---- ----
% ID_MID ---- ---- ---- ----

%%% USER CODE: MORPHOGEN INTERACTIONS

% In this section you may modify the mesh in any way that does not
% Section 4
% alter the set of nodes.

% Use the same pattern for both submodels
RangeTip=(m.nodes(:,1)<-0.8)&...
(abs(m.nodes(:,2))<0.2);
RangeMid=(m.nodes(:,1)<=0.5)&...
(m.nodes(:,1)>-0.5)&...
(abs(m.nodes(:,2))<0.3);
RangeTops=(m.nodes(:,1)<=max(m.nodes(:,1))&...
(m.nodes(:,1)>0.5)&...
(abs(m.nodes(:,2))>0.3));
if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.
switch modelname
 case 'PolariserBased' % 
% One way to set up a morphogen gradient is by ...
% Setting up a gradient by clamping the ends (execute only once)
P(RangeTip)=0;
P(RangeMid)=0.5;
P(RangeTops)=1;
id_plusorg_p=P;
id_minusorg_p(RangeTip)=1;
m.morphogenclamp( RangeTops|RangeTip|RangeMid, polariser_i ) = 1;
m = leaf_mgen_conductivity( m, 'POLARISER', 0.1 ); %specifies the diffusion rate of polariser
m = leaf_mgen_absorption( m, 'POLARISER', 0.0 ); % specifies degradation rate of polariser
 case 'DifferentialGrowthBased' % 
P(:)=0;
% One way to set up a morphogen gradient is by ...
% Setting up a gradient by clamping the ends (execute only once)
s_growth_p(RangeTip)=1;
s_growth_p(RangeMid)=0.05;
s_growth_p(RangeTops)=0.8;
m.morphogenclamp( RangeTops|RangeTip|RangeMid, s_growth_i ) = 1;
m = leaf_mgen_conductivity( m, 's_growth', 0.001 ); %specifies the diffusion rate of polariser
m = leaf_mgen_absorption( m, 's_growth', 0.0 ); % specifies degradation rate of polariser
end
end
BasicGrowth=0.01;
switch modelname
 case 'PolariserBased' %
% Every equation to be formatted should end with an at-at Eqn N comment.
kapar_p(:) = BasicGrowth; % when isotropic this will be 0.005
kaper_p(:) = 0.0; % when isotropic this will be 0.005
kbpar_p(:) = BasicGrowth; % when isotropic this will be 0.005
kbper_p(:) = 0.0; % when isotropic this will be 0.005
knor_p(:) = 0; % thickness
 case 'DifferentialGrowthBased' % 
% Every equation to be formatted should end with an at-at Eqn N comment.
kapar_p(:) = BasicGrowth*s_growth_p; %0.01; % when isotropic this will be 0.005
kaper_p(:) = BasicGrowth*s_growth_p; %0.0; % when isotropic this will be 0.005
kbpar_p(:) = BasicGrowth*s_growth_p; %0.01; % when isotropic this will be 0.005
kbper_p(:) = BasicGrowth*s_growth_p; %0.0; % when isotropic this will be 0.005
knor_p(:) = 0; % thickness
end
v_kareal_p=kapar_p+kaper_p; % total specified areal growth
% Section 5
%%% 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_plusorg_i) = id_plusorg_p;
m.morphogens(:,id_minusorg_i) = id_minusorg_p;
m.morphogens(:,v_kareal_i) = v_kareal_p;
m.morphogens(:,id_tip_i) = id_tip_p;
m.morphogens(:,id_top_i) = id_top_p;
m.morphogens(:,s_growth_i) = s_growth_p;
m.morphogens(:,id_mid_i) = id_mid_p;

%%% USER CODE: FINALISATION

%%% END OF USER CODE: FINALISATION

end

%%% USER CODE: SUBFUNCTIONS

% Section 6
function m = local_setproperties( m )
end

Tutorial on two romantic hearts - Revision history

AndrewBangham: Created page with 'Back to GFtbox Tutorial pages We illustrate the practical advantage of having submodels within a project and an important con…'

AndrewBangham: Created page with 'Back to GFtbox Tutorial pages

We illustrate the practical advantage of having submodels within a project and an important con…'