GPT tut interaction 20110530 first edit: Difference between revisions
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Revision as of 12:06, 30 May 2011
function m = gpt_tut_interaction_20110530( m )
%m = gpt_tut_interaction_20110530( m )
% Morphogen interaction function.
% Written at 2011-05-30 09:42:07.
% GFtbox revision 0, .
% 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
% In this section you may modify the mesh in any way whatsoever.
if (Steps(m)==0) && m.globalDynamicProps.doinit % First iteration
% Zero out a lot of stuff to create a blank slate.
% If no morphogens are set in the GUI it may be useful to
% zero some arrays by uncommenting the following.
% m.morphogens(:) = 0;
% m.morphogenclamp(:) = 0;
% m.mgen_production(:) = 0;
% m.mgen_absorption(:) = 0;
% m.seams(:) = false;
% m.mgen_dilution(:) = false;
% Set up names for variant models. Useful for running multiple models on a cluster.
m.userdata.ranges.modelname.range = { 'MODEL1', 'MODEL2' }; % 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));
switch modelname
case 'MODEL1'
% Set up the parameters (e.g. mutations) for this model here.
case 'MODEL2'
% Set up the parameters (e.g. mutations) for this model here.
otherwise
% If you reach here, you probably forgot a case.
end
% More examples of code for all iterations.
% Set priorities for simultaneous plotting of multiple morphogens, if desired.
% m = leaf_mgen_plotpriority( m, {'MGEN1', 'MGEN2'}, [1,2], [0.5,0.75] );
% Set colour of polariser gradient arrows.
% m = leaf_plotoptions(m,'highgradcolor',[0,0,0],'lowgradcolor',[1,0,0]);
% setup a multiplot of the following morphogens
% m = leaf_plotoptions( m, 'morphogen', {'V_PROFILE1','V_PROFILE2','KAPAR','S_LEFTRIGHT'});
% to plot polariser on the A side and resultant areal growth rate on the B side:
% m = leaf_plotoptions( m, 'morphogenA', 'POLARISER', ...
% 'outputquantityB', 'resultantgrowthrate', ...
% 'outputaxesB', 'areal' );
% monitor properties of vertices must be done here - so that it reports newly equilibrated levels
% m=leaf_profile_monitor(m,... % essential
% 'REGIONLABELS',{'V_PROFILE1','V_PROFILE2'},... % essential
% 'MORPHOGENS',{'S_LEFTRIGHT','S_CENTRE'},... % optional (one element per REGIONLABEL)
% 'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')
%%% 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_plusorg_i,id_plusorg_p,id_plusorg_a,id_plusorg_l] = getMgenLevels( m, 'ID_PLUSORG' );
[id_negorg_i,id_negorg_p,id_negorg_a,id_negorg_l] = getMgenLevels( m, 'ID_NEGORG' );
[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_PLUSORG ---- ---- ---- ----
% ID_NEGORG ---- ---- ---- ----
% ID_A ---- ---- ---- ----
% ID_B ---- ---- ---- ----
%%% USER CODE: MORPHOGEN INTERACTIONS
% In this section you may modify the mesh in any way that does not
% alter the set of nodes.
if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.
% Put any code here that should only be performed at the start of
% the simulation, for example, to set up initial morphogen values.
% m.nodes is the set of vertex positions, an N by 3 array if there
% are N vertices. Row number K contains the X, Y, and Z
% coordinates of the Kth vertex. To obtain a list of the X
% coordinates of every vertex, write m.nodes(:,1). The Y
% coordinates are given by m.nodes(:,2) and the Z coordinates by
% m.nodes(:,3).
% Set up a morphogen promoter (_p suffix) region where x values are minimum
% id_prox_p(m.nodes(:,1)==min(m.nodes(:,1)))=1;
% if the morphogen level (_l suffix) is to be used in this iteration
% set the level using the morphogen activity (_a suffix).
% id_prox_l=id_prox_p * id_prox_a; % when a mutation is specified in the GUI
% the activity (_a) is set to zero
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
% One way to set up a morphogen gradient is by ...
% Setting up a gradient by clamping the ends (execute only once)
% P=id_prox_p;
% m.morphogenclamp( ((id_prox_p==1)|(id_dist_p==1)), polariser_i ) = 1;
% m = leaf_mgen_conductivity( m, 'POLARISER', 0.01 ); %specifies the diffusion rate of polariser
% m = leaf_mgen_absorption( m, 'POLARISER', 0.1 ); % specifies degradation rate of polariser
% Fixing vertices, i.e. fix z for the base to prevent base from moving up or down
% m=leaf_fix_vertex(m,'vertex',find(id_prox_p==1),'dfs','z');
% To cut the mesh, set a temporary morphogen to 1 in places to cut
% seams=zeros(size(P));
% seams(indexes to places to cut)=1;
% m=leaf_set_seams(m,seams);
end
% Second way to generate a gradient
% generating (+) and sinking (-) a diffusing signal (in this case polariser)
% m.mgen_production( :, polariser_i ) = + 5*s_spur_p - P .* id_dist_p;
% Monitor growth by scattering discs that deform over time (c.f. inducing biological clones)
% (CARE - if the canvas is flat ensure that Plot:Hide Thickness is true,
% because a quirk of the Matlab z-buffer means that they can get hidden by mistake)
% if (340>realtime-dt) && (340<realtime+dt) % discs to be added at realtime==340
% m = leaf_makesecondlayer( m, ... % This function adds discs that represent transformed cells.
% 'mode', 'each', ... % Make discs randomly scattered over the canvas.
% 'relarea', 1/16000, ... % Each discs has area was 1/16000 of the initial area of the canvas.
% 'probpervx', 'V_FLOWER', ... % induce discs over whole canvas (V_FLOWER is 1 over whole canvas)
% 'numcells',4500,...%number of discs (that will become ellipses)
% 'sides', 6, ... % Each discs is approximated as a 6-sided regular polygon.
% 'colors', [0.5 0.5 0.5], ... % Default colour is gray but
% 'colorvariation',1,... % Each disc is a random colour
% 'add', true ); % These discs are added to any discs existing already
% end
% Directives for creating latex representation directly from Matlab code
% not fully implemented yet but will use @@ directives
% @@at t
% @@before t
% @@after t
% @@between t1 t2
% % If you want to define different phases according to the absolute
% % time, create a morphogen for each phase and modulate
% % expressions using the morphogen
% % like. For example:
% if (realtime < 10) % first growth phase
% f_firstgrowth_p = 1;
% else
% f_firstgrowth_p = 0;
% end
% if (realtime >= 10) % second growth phase
% f_secondgrowth_p = 1;
% else
% f_secondgrowth_p = 0;
% end
%
% % If you want one morphogen to affect others only during a certain
% % phase, write something like:
%
% mgen_a_p = f_firstgrowth_p .* (various terms); % will zero except in firstgrowth
% Code common to all models.
% @@PRN Polariser Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% @@GRN Gene Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% @@KRN Growth Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% Code for specific models.
switch modelname
case 'MODEL1' % @@model MODEL1
% @@PRN Polariser Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% P(:) = ... % @@ Eqn xx
% @@GRN Gene Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% @@KRN Growth Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% kapar_p(:) = 0; % @@ Eqn xx
% kaper_p(:) = 0; % @@ Eqn xx
% kbpar_p(:) = 0; % @@ Eqn xx
% kbper_p(:) = 0; % @@ Eqn xx
% knor_p(:) = 0; % @@ Eqn xx
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
case 'MODEL2' % @@model MODEL2
% @@PRN Polariser Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% P(:) = ... % @@ Eqn xx
% @@GRN Gene Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% @@KRN Growth Regulatory Network
% Every equation to be formatted should end with an at-at Eqn N comment.
% kapar_p(:) = 0; % @@ Eqn xx
% kaper_p(:) = 0; % @@ Eqn xx
% kbpar_p(:) = 0; % @@ Eqn xx
% kbper_p(:) = 0; % @@ Eqn xx
% knor_p(:) = 0; % @@ Eqn xx
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
otherwise
% If this happens, maybe you forgot a model.
end
%%% 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_negorg_i) = id_negorg_p;
m.morphogens(:,id_a_i) = id_a_p;
m.morphogens(:,id_b_i) = id_b_p;
%%% USER CODE: FINALISATION
% In this section you may modify the mesh in any way whatsoever.
% If needed force FE to subdivide (increase number FE's) here
% if realtime==280+dt
% m = leaf_subdivide( m, 'morphogen','id_vent',...
% 'min',0.5,'max',1,...
% 'mode','mid','levels','all');
% end
% Cut the mesh along the seams (see above)
% if m.userdata.CutOpen==1
% m=leaf_dissect(m);
% m.userdata.CutOpen=2;
% Relax accumulated stresses slowly i.e. 0.95 to 0.999
% m = leaf_setproperty( m, 'freezing', 0.999 );
% end
%%% END OF USER CODE: FINALISATION
end
%%% USER CODE: SUBFUNCTIONS
function m = local_setproperties( m )
% This function is called at time zero in the INITIALISATION section of the
% interaction function. It provides commands to set each of the properties
% that are contained in m.globalProps. Uncomment whichever ones you would
% like to set yourself, and put in whatever value you want.
%
% Some of these properties are for internal use only and should never be
% set by the user. At some point these will be moved into a different
% component of m, but for the present, just don't change anything unless
% you know what it is you're changing.
% m = leaf_setproperty( m, 'trinodesvalid', true );
% m = leaf_setproperty( m, 'prismnodesvalid', true );
% m = leaf_setproperty( m, 'thicknessRelative', 0.020000 );
% m = leaf_setproperty( m, 'thicknessArea', 0.000000 );
% m = leaf_setproperty( m, 'thicknessMode', 'physical' );
% m = leaf_setproperty( m, 'activeGrowth', 1.000000 );
% m = leaf_setproperty( m, 'displayedGrowth', 1.000000 );
% m = leaf_setproperty( m, 'displayedMulti', [] );
% m = leaf_setproperty( m, 'allowNegativeGrowth', true );
% m = leaf_setproperty( m, 'usePrevDispAsEstimate', true );
% m = leaf_setproperty( m, 'perturbInitGrowthEstimate', 0.000010 );
% m = leaf_setproperty( m, 'perturbRelGrowthEstimate', 0.010000 );
% m = leaf_setproperty( m, 'perturbDiffusionEstimate', 0.000100 );
% m = leaf_setproperty( m, 'resetRand', false );
% m = leaf_setproperty( m, 'mingradient', 0.000000 );
% m = leaf_setproperty( m, 'relativepolgrad', false );
% m = leaf_setproperty( m, 'usefrozengradient', true );
% m = leaf_setproperty( m, 'userpolarisation', false );
% m = leaf_setproperty( m, 'thresholdsq', 0.000841 );
% m = leaf_setproperty( m, 'splitmargin', 1.400000 );
% m = leaf_setproperty( m, 'splitmorphogen', );
% m = leaf_setproperty( m, 'thresholdmgen', 0.500000 );
% m = leaf_setproperty( m, 'bulkmodulus', 1.000000 );
% m = leaf_setproperty( m, 'unitbulkmodulus', true );
% m = leaf_setproperty( m, 'poissonsRatio', 0.300000 );
% m = leaf_setproperty( m, 'starttime', 0.000000 );
% m = leaf_setproperty( m, 'timestep', 0.010000 );
% m = leaf_setproperty( m, 'timeunitname', );
% m = leaf_setproperty( m, 'distunitname', 'mm' );
% m = leaf_setproperty( m, 'scalebarvalue', 0.000000 );
% m = leaf_setproperty( m, 'validateMesh', true );
% m = leaf_setproperty( m, 'rectifyverticals', false );
% m = leaf_setproperty( m, 'allowSplitLongFEM', true );
% m = leaf_setproperty( m, 'longSplitThresholdPower', 0.000000 );
% m = leaf_setproperty( m, 'allowSplitBentFEM', false );
% m = leaf_setproperty( m, 'allowSplitBio', true );
% m = leaf_setproperty( m, 'allowFlipEdges', false );
% m = leaf_setproperty( m, 'allowElideEdges', true );
% m = leaf_setproperty( m, 'mincellangle', 0.200000 );
% m = leaf_setproperty( m, 'alwaysFlat', 0.000000 );
% m = leaf_setproperty( m, 'flattenforceconvex', true );
% m = leaf_setproperty( m, 'flatten', false );
% m = leaf_setproperty( m, 'flattenratio', 1.000000 );
% m = leaf_setproperty( m, 'useGrowthTensors', false );
% m = leaf_setproperty( m, 'plasticGrowth', false );
% m = leaf_setproperty( m, 'totalinternalrotation', 0.000000 );
% m = leaf_setproperty( m, 'stepinternalrotation', 2.000000 );
% m = leaf_setproperty( m, 'showinternalrotation', false );
% m = leaf_setproperty( m, 'performinternalrotation', false );
% m = leaf_setproperty( m, 'internallyrotated', false );
% m = leaf_setproperty( m, 'maxFEcells', 0 );
% m = leaf_setproperty( m, 'inittotalcells', 0 );
% m = leaf_setproperty( m, 'bioApresplitproc', );
% m = leaf_setproperty( m, 'bioApostsplitproc', );
% m = leaf_setproperty( m, 'maxBioAcells', 0 );
% m = leaf_setproperty( m, 'maxBioBcells', 0 );
% m = leaf_setproperty( m, 'colors', (6 values) );
% m = leaf_setproperty( m, 'colorvariation', 0.050000 );
% m = leaf_setproperty( m, 'colorparams', (12 values) );
% m = leaf_setproperty( m, 'freezing', 0.000000 );
% m = leaf_setproperty( m, 'canceldrift', false );
% m = leaf_setproperty( m, 'mgen_interaction', );
% m = leaf_setproperty( m, 'mgen_interactionName', 'gpt_tut_interaction_20110530' );
% m = leaf_setproperty( m, 'allowInteraction', true );
% m = leaf_setproperty( m, 'interactionValid', true );
% m = leaf_setproperty( m, 'gaussInfo', (unknown type struct) );
% m = leaf_setproperty( m, 'stitchDFs', [] );
% m = leaf_setproperty( m, 'D', (36 values) );
% m = leaf_setproperty( m, 'C', (36 values) );
% m = leaf_setproperty( m, 'G', (6 values) );
% m = leaf_setproperty( m, 'solver', 'cgs' );
% m = leaf_setproperty( m, 'solverprecision', 'double' );
% m = leaf_setproperty( m, 'solvertolerance', 0.001000 );
% m = leaf_setproperty( m, 'solvertolerancemethod', 'norm' );
% m = leaf_setproperty( m, 'diffusiontolerance', 0.000010 );
% m = leaf_setproperty( m, 'allowsparse', true );
% m = leaf_setproperty( m, 'maxIters', 0 );
% m = leaf_setproperty( m, 'maxsolvetime', 1000.000000 );
% m = leaf_setproperty( m, 'cgiters', 0 );
% m = leaf_setproperty( m, 'simsteps', 0 );
% m = leaf_setproperty( m, 'stepsperrender', 0 );
% m = leaf_setproperty( m, 'growthEnabled', true );
% m = leaf_setproperty( m, 'diffusionEnabled', true );
% m = leaf_setproperty( m, 'flashmovie', false );
% m = leaf_setproperty( m, 'makemovie', false );
% m = leaf_setproperty( m, 'moviefile', );
% m = leaf_setproperty( m, 'codec', 'None' );
% m = leaf_setproperty( m, 'autonamemovie', true );
% m = leaf_setproperty( m, 'overwritemovie', false );
% m = leaf_setproperty( m, 'framesize', [] );
% m = leaf_setproperty( m, 'mov', [] );
% m = leaf_setproperty( m, 'jiggleProportion', 1.000000 );
% m = leaf_setproperty( m, 'cvtperiter', 0.200000 );
% m = leaf_setproperty( m, 'boingNeeded', false );
% m = leaf_setproperty( m, 'initialArea', 0.031326 );
% m = leaf_setproperty( m, 'bendunitlength', 0.176992 );
% m = leaf_setproperty( m, 'targetRelArea', 1.000000 );
% m = leaf_setproperty( m, 'defaultinterp', 'min' );
% m = leaf_setproperty( m, 'readonly', false );
% m = leaf_setproperty( m, 'projectdir', 'D:\ab\Matlab stuff' );
% m = leaf_setproperty( m, 'modelname', 'GPT_tut_interaction_20110530' );
% m = leaf_setproperty( m, 'allowsave', true );
% m = leaf_setproperty( m, 'addedToPath', false );
% m = leaf_setproperty( m, 'bendsplit', 0.300000 );
% m = leaf_setproperty( m, 'usepolfreezebc', false );
% m = leaf_setproperty( m, 'dorsaltop', true );
% m = leaf_setproperty( m, 'defaultazimuth', -45.000000 );
% m = leaf_setproperty( m, 'defaultelevation', 33.750000 );
% m = leaf_setproperty( m, 'defaultroll', 0.000000 );
% m = leaf_setproperty( m, 'defaultViewParams', (unknown type struct) );
% m = leaf_setproperty( m, 'comment', );
% m = leaf_setproperty( m, 'legendTemplate', '%T: %q\n%m' );
% m = leaf_setproperty( m, 'bioAsplitcells', true );
% m = leaf_setproperty( m, 'bioApullin', 0.142857 );
% m = leaf_setproperty( m, 'bioAfakepull', 0.202073 );
% m = leaf_setproperty( m, 'interactive', false );
% m = leaf_setproperty( m, 'coderevision', 0 );
% m = leaf_setproperty( m, 'coderevisiondate', );
% m = leaf_setproperty( m, 'modelrevision', 0 );
% m = leaf_setproperty( m, 'modelrevisiondate', );
% m = leaf_setproperty( m, 'savedrunname', );
% m = leaf_setproperty( m, 'savedrundesc', );
% m = leaf_setproperty( m, 'vxgrad', (108 values) );
% m = leaf_setproperty( m, 'lengthscale', 0.200000 );
end
% Here you may write any functions of your own, that you want to call from
% the interaction function, but never need to call from outside it.
% Remember that they do not have access to any variables except those
% that you pass as parameters, and cannot change anything except by
% returning new values as results.
% Whichever section they are called from, they must respect the same
% restrictions on what modifications they are allowed to make to the mesh.
% For example:
% function m = do_something( m )
% % Change m in some way.
% end
% Call it from the main body of the interaction function like this:
% m = do_something( m );