Default MTtbox interaction function
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Comments are in green - this web version of the matlab file was created using the DArT_Toolbox tool:
webify_interaction_function('MT_Tues_20120501.m')
function data = MT_Tues_20120501( data, before )
if nargin < 1, return; end
%
%
% extract factors from structure
for i=1:size( data.factorprops.Concentration,2)
factname=lower(data.factorprops.Index2Name{i});
eval([[factname,'_p'],'=reshape(','data.factorprops.Concentration(:,i),[ data.cellprops.cellsize]);']);
eval([[factname,'_i'],'=','data.factorprops.Name2Index.(factname);']);
end
% insert model in here
% data=setupDiffusion(data,'Factorname','s_micplm','DiffK',[0.2,0.2],...
% 'RegionLists',{{'cytoplasm','vacuole','cell_wall'},{'plasma_membrane','microtubules'}});
% data=setupDiffusion(data,'Factorname','id_micplm','DiffK',[0,0],...
% 'RegionLists',{{'cytoplasm','vacuole','cell_wall'},{'plasma_membrane','microtubules'}});
% data.factorprops.DiffusionConst(:,1)=0.1; % This should be superceed by the above
% data.factorprops.DiffusionConst(:,2)=0.05;% This should be superceed by the above
if data.iterations<0
% insert initialisation code here - use Initialise button to jump to here
% modify default cell specifications, etc. to modify how the cell volume is partitioned, e.g.
% data.organelleprops.plasma_membrane.size=0.95; % fraction of longest dimension
% data.organelleprops.cytoplasm.size=0.80;
% data.organelleprops.vacuole.size=0.4;
% data.organelleprops.microtubules.nuclspont=0.0012; % observed nucleations per square (cubic) micron per sec
elseif data.iterations==0
% insert startup code here - use Restart button to jump to here
%% setup MT size
%if data.cellprops.cellsize(1)>25
% data=mtSETprops(data,'microtubules','size',0.01,'microtubules','growthrate',0.025);
% data=mtSETprops(data,'microtubules','shrinkrate',0.005);
%end
else
%id_micplm_p(:)=0; % clear
%id_micplm_p(data.cellprops.Vol==data.organelleprops.cytoplasm.Label)=0.8; % set cytoplasm region to 1
%id_micplm_p(round(data.cellprops.cellsize(1)/3):end,:,:)=0; % then set right hand end back to zero
%s_micplm_p(id_micplm_p>0.1)=0.1;
%% limit spontaneous nucleation to a region specified by id_micplm_p
% data.organelleprops.microtubules.nuclspont=id_micplm_p;
%data.cellprops.colourType=0; % set to 1 if colour is to be specified by individual MT property
%Work through all the microtubules updating properties depending on flags
%Average number of MT's present is observed to be about 80 i.e. 80/300 square microns (say 1 micron thick
%so ~0.25 per square (cubic) micron
for i_MT=1:length(data.working.dyn.microtubules.Org)
MT=data.working.dyn.microtubules.Org(i_MT);
% MTtbox monitors ...
% MT.Type
% MT.Age
% MT.PauseDuration
% MT.TimeNucleated
% MT.Alive=true;
% MT.Growing=true;
% MT.Shrinking=true;
% MT.Catastrophe=false;
% MT.BoundPLM=false;
% MT.PLMBindVertNums=[];
% MT.BoundMic=false;
% MT.MTBindVertNums=[];
% MT.BoundVac=false;
% MT.VacBindVertNums=[];
% MT.Hit=struct('Type',,'ID',[]);
% MT.HitMe=struct('Type',,'ID',[]);
% MT.Props.growthrate
% MT.Props.shrinkrate
% MT.Props.maxbend
% MT.Props.maxAge
% MT.Props.nuclspont
% MT.Props.nuclonMT
% Make changes here, i.e.
% diffs=diff(MT.Verts).^2; % calculate length of MT
% MTlength=sum(sqrt(sum(diffs')'))*data.cellprops.micronsPerVoxelEdge; % microns
% if MTlength>0.5
% MT.Props.nuclonMT=min(1,0.4*MTlength); % observed approx. 0.007 per micron per sec
% else
% MT.Props.nuclonMT=0;
% end
%ageMT=data.working.CellAge;% seconds
%maxAgeColour=20;
%MT.Props.FaceColor=[max(0,min(1,1-ageMT/maxAgeColour)), 0.5, max(0,min(1,ageMT/maxAgeColour))];
%if MT.BoundPLM && MT.Growing % hit plasma_membrane and aligned
%elseif MT.BoundPLM && ~MT.Growing % hit plasma_membrane and NOT aligned
%end
%if MT.BoundMic && MT.Growing % hit another microtubule and aligned
%elseif MT.BoundMic && ~MT.Growing % hit another microtubule and NOT aligned
%end
%if MT.BoundVac && MT.Growing % hit vacuole membrane and aligned
%elseif MT.BoundVac && ~MT.Growing % hit vacuole membrane and NOT aligned
%end
% Keep the following
% Clear flags from collision detector
MT.BoundPLM=false;
MT.BoundMic=false;
MT.BoundVac=false;
data.working.dyn.microtubules.Org(i_MT)=MT;
end
end
% put factors back into structure
for i=1:size( data.factorprops.Concentration,2)
factname=lower(data.factorprops.Index2Name{i});
eval(['data.factorprops.Concentration(:,i)=',[factname,'_p(:);']]);
end
end
% This space intentionally left blank.
% Default factor parameters
% Default organelle parameters
% cell_wall.size =0.000000
% cell_wall.offset =0.500000
% cell_wall.micronthick =0.100000
% cell_wall.minvox =1.000000
% cell_wall.FaceColor =[1.000000,0.000000,1.000000,]
% cell_wall.FaceAlpha =0.010000
% cell_wall.Label =-5.000000
% cell_wall.isLayer =1.000000
% cell_wall.Static =1.000000
% cell_wall.InUse =1.000000
%plasma_membrane.size =0.000000
%plasma_membrane.offset =0.500000
%plasma_membrane.micronthick =0.010000
%plasma_membrane.minvox =3.000000
%plasma_membrane.FaceColor =[1.000000,1.000000,0.000000,]
%plasma_membrane.FaceAlpha =0.020000
%plasma_membrane.Label =-4.000000
%plasma_membrane.isLayer =1.000000
%plasma_membrane.Static =1.000000
%plasma_membrane.InUse =1.000000
% cytoplasm.size =0.000000
% cytoplasm.offset =0.500000
% cytoplasm.micronthick =1.000000
% cytoplasm.minvox =5.000000
% cytoplasm.FaceColor =[0.000000,1.000000,0.000000,]
% cytoplasm.FaceAlpha =0.020000
% cytoplasm.Label =0.000000
% cytoplasm.isLayer =1.000000
% cytoplasm.Static =1.000000
% cytoplasm.InUse =1.000000
% microtubules.size =0.025000
% microtubules.minvoxel =3.000000
% microtubules.growthrate =0.100000
% microtubules.shrinkrate =0.010000
% microtubules.maxbend =40.000000
% microtubules.MaxAngle =20.000000
% microtubules.maxAge =0.000000
% microtubules.nuclspont =0.050000
% microtubules.nuclonMT =0.090000
% microtubules.probCatastrophe=0.300000
% microtubules.FaceColor =[0.000000,0.000000,1.000000,]
% microtubules.FaceAlpha =0.400000
% microtubules.Label =-6.000000
% microtubules.isLayer =0.000000
% microtubules.Static =0.000000
% microtubules.InUse =1.000000
% vacuole.size =0.200000
% vacuole.offset =0.500000
% vacuole.micronthick =1.000000
% vacuole.minvox =0.000000
% vacuole.FaceColor =[1.000000,1.000000,0.000000,]
% vacuole.FaceAlpha =0.300000
% vacuole.Label =-3.000000
% vacuole.isLayer =0.000000
% vacuole.Static =1.000000
% vacuole.InUse =1.000000
% Default cell parameters
% cellprops.shape ='Rect:1:1:1'
% cellprops.sheetmodel =0
% cellprops.maxLengthMicrons=10
% cellprops.secondsPerStep =1
% cellprops.micronsPerVoxelEdge=0.400000
% cellprops.cubicMicronsPerVoxel=0.064000
% cellprops.cellsize =[25,25,25,]
% cellprops.colourType =1
% cellprops.Vol =[-1,-1,-1,-1, ... ]
% cellprops.Smooth ='None'
% cellprops.dynamic ='microtubules'
% cellprops.bound_distance =5
% cellprops.collide_distance=10
% cellprops.% vacuole.Vol=struct
% vacuole.EdgeVol=struct
% cellprops.% cell_wall.Vol=struct
% cell_wall.EdgeVol=struct
% cellprops.% plasma_membrane.Vol=struct
% plasma_membrane.EdgeVol=struct
% cellprops.% cytoplasm.Vol=struct
% cytoplasm.EdgeVol=struct
% cytoplasm.Indexes=struct
% cellprops.% Diameter.microtubules=struct
% cellprops.% microtubules.Vol=struct
% microtubules.Offsets=struct