Full freshly minted interaction function
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Tutorial on the basic interaction function
The large number of comments do two things. Firstly, they provide guidence on how to structure a growth model - in other words how one might organise thoughts on how things grow - the polarity regulation network, the gene regulation network and the specified growth regulation network. Secondly, they help us remember how to do certain things without having to look them up in the manual (that is not always complete and up to date). It is easier to delete what is not wanted than to look up and add what is wanted.
Remember: a GFtbox model comprises two parts, the Mesh and the Interaction function. At the point that the interaction function is created the Mesh exists (shape and general physical properties) but the regulatory systems do not - it is these that you add to the interaction function. A loose analogy is to say that the Mesh corresponds to the cell membranes and cytoplasm (the structure) and the Interaction function corresponds to the nucleus and DNA. You need both to grow - and they must be compatible with each other.
This file is output automatically on clicking Panel: Edit in a newly saved project.
Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.
The code has been divided into Sections to help with the tutorial.
Section 1 function m = gpt_tut_fresh_interaction_function_20110530( m ) %m = gpt_tut_fresh_interaction_function_20110530( m ) % Morphogen interaction function. % Written at 2011-05-30 20:10:22. % 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; 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 % 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 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' ); % 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 ---- ---- ---- ---- % STRAINRET ---- ---- ---- ---- % ARREST ---- ---- ---- ---- %%% 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. 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 % 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 Section 5 % 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 Section 6 % 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 Section 7 % % 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 Section 8 % 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. Section 9 % Code for specific models. switch modelname Section 10 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 Section 11 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 otherwise % If this happens, maybe you forgot a model. end Section 12 %%% 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; %%% USER CODE: FINALISATION % In this section you may modify the mesh in any way whatsoever. Section 13 % 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 Section 14 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', 0.200000 ); % 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', 0.227223 ); % 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_fresh_interaction_function_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', 3.105828 ); % m = leaf_setproperty( m, 'bendunitlength', 1.762336 ); % 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_fresh_interaction_function_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', 2.000000 ); end Section 15 % 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: Section 16 % 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 );