MTtbox documentation: Difference between revisions

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|width="400pt"|(Comments are in green - this web version of the matlab file is created using webify_interaction_function('MT_Edinb_20120427.m')).<br><br>
|width="400pt"|(Comments are in green - this web version of the matlab file is created using webify_interaction_function('MT_Edinb_20120427.m')).<br><br>
The default file is largely a copy of''' MTtbox_BoilerPlate.txt''' which should be updated to reflect the latest ideas on how to build the function.  
The default file is largely a copy of''' MTtbox_BoilerPlate.txt''' which should be updated to reflect the latest ideas on how to build the function.  
<br><br>
<br><br>  
  function data = MT_Tues_20120501( data, before )
[[Default MTtbox interaction function|Initial MTtbox interaction function is shown here]]
    if nargin < 1, return; end
<span style="color: Green">% </span>
<span style="color: Green">%</span>
<span style="color: Green">% extract factors from structure</span>
    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
<span style="color: Green">% insert model in here</span>
<span style="color: Green">%    data=setupDiffusion(data,'Factorname','s_micplm','DiffK',[0.2,0.2],...</span>
<span style="color: Green">%        'RegionLists',{{'cytoplasm','vacuole','cell_wall'},{'plasma_membrane','microtubules'}});</span>
<span style="color: Green">%    data=setupDiffusion(data,'Factorname','id_micplm','DiffK',[0,0],...</span>
<span style="color: Green">%        'RegionLists',{{'cytoplasm','vacuole','cell_wall'},{'plasma_membrane','microtubules'}});</span>
<span style="color: Green">%    data.factorprops.DiffusionConst(:,1)=0.1; % This should be superceed by the above</span>
<span style="color: Green">%    data.factorprops.DiffusionConst(:,2)=0.05;% This should be superceed by the above</span>
    if data.iterations<0
        <span style="color: Green">% insert initialisation code here - use Initialise button to jump to here</span>
        <span style="color: Green">% modify default cell specifications, etc. to modify how the cell volume is partitioned, e.g.</span>
        <span style="color: Green">% data.organelleprops.plasma_membrane.size=0.95; % fraction of longest dimension</span>
        <span style="color: Green">% data.organelleprops.cytoplasm.size=0.80;</span>
        <span style="color: Green">% data.organelleprops.vacuole.size=0.4;</span>
        <span style="color: Green">% data.organelleprops.microtubules.nuclspont=0.0012; % observed nucleations per square (cubic) micron per sec</span>
    elseif data.iterations==0
        <span style="color: Green">% insert startup code here - use Restart button to jump to here</span>
        <span style="color: Green">%% setup MT size</span>
        <span style="color: Green">%if data.cellprops.cellsize(1)>25</span>
        <span style="color: Green">%    data=mtSETprops(data,'microtubules','size',0.01,'microtubules','growthrate',0.025);</span>
        <span style="color: Green">%    data=mtSETprops(data,'microtubules','shrinkrate',0.005);</span>
        <span style="color: Green">%end</span>
    else
        <span style="color: Green">%id_micplm_p(:)=0; % clear</span>
        <span style="color: Green">%id_micplm_p(data.cellprops.Vol==data.organelleprops.cytoplasm.Label)=0.8; % set cytoplasm region to 1</span>
        <span style="color: Green">%id_micplm_p(round(data.cellprops.cellsize(1)/3):end,:,:)=0; % then set right hand end back to zero</span>
        <span style="color: Green">%s_micplm_p(id_micplm_p>0.1)=0.1;</span>
        <span style="color: Green">%%      limit spontaneous nucleation to a region specified by id_micplm_p</span>
        <span style="color: Green">%        data.organelleprops.microtubules.nuclspont=id_micplm_p;</span>
        <span style="color: Green">%data.cellprops.colourType=0; % set to 1 if colour is to be specified by individual MT property</span>
        <span style="color: Green">%Work through all the microtubules updating properties depending on flags</span>
        <span style="color: Green">%Average number of MT's present is observed to be about 80 i.e. 80/300 square microns (say 1 micron thick</span>
        <span style="color: Green">%so ~0.25 per square (cubic) micron</span>
        for i_MT=1:length(data.working.dyn.microtubules.Org)
            MT=data.working.dyn.microtubules.Org(i_MT);
            <span style="color: Green">% MTtbox monitors ...</span>
            <span style="color: Green">% MT.Age</span>
            <span style="color: Green">% MT.PauseDuration</span>
            <span style="color: Green">% MT.TimeNucleated</span>
            <span style="color: Green">% MT.Alive=true;</span>
            <span style="color: Green">% MT.Growing=true;</span>
            <span style="color: Green">% MT.Shrinking=true;</span>
            <span style="color: Green">% MT.Catastrophe=false;</span>
            <span style="color: Green">% MT.BoundPLM=false;</span>
            <span style="color: Green">% MT.PLMBindVertNums=[];</span>
            <span style="color: Green">% MT.BoundMic=false;</span>
            <span style="color: Green">% MT.MTBindVertNums=[];</span>
            <span style="color: Green">% MT.BoundVac=false;</span>
            <span style="color: Green">% MT.VacBindVertNums=[];    </span>
            <span style="color: Green">% MT.Hit=struct('Type','','ID',[]);  </span>
            <span style="color: Green">% MT.HitMe=struct('Type','','ID',[]); </span>
            <span style="color: Green">% MT.Props.growthrate</span>
            <span style="color: Green">% MT.Props.shrinkrate</span>
            <span style="color: Green">% MT.Props.maxbend</span>
            <span style="color: Green">% MT.Props.maxAge</span>
            <span style="color: Green">% MT.Props.nuclspont</span>
            <span style="color: Green">% MT.Props.nuclonMT</span>
            <span style="color: Green">% Make changes here, i.e.</span>
            <span style="color: Green">% diffs=diff(MT.Verts).^2; % calculate length of MT</span>
            <span style="color: Green">% MTlength=sum(sqrt(sum(diffs')'))*data.cellprops.micronsPerVoxelEdge; % microns</span>
            <span style="color: Green">% if MTlength>0.5</span>
            <span style="color: Green">%    MT.Props.nuclonMT=min(1,0.4*MTlength); % observed approx. 0.007 per micron per sec</span>
            <span style="color: Green">% else</span>
            <span style="color: Green">%    MT.Props.nuclonMT=0;</span>
            <span style="color: Green">% end</span>
            <span style="color: Green">%ageMT=data.working.CellAge;% seconds</span>
            <span style="color: Green">%maxAgeColour=20;</span>
            <span style="color: Green">%MT.Props.FaceColor=[max(0,min(1,1-ageMT/maxAgeColour)), 0.5, max(0,min(1,ageMT/maxAgeColour))];</span>
            <span style="color: Green">%if  MT.BoundPLM && MT.Growing  % hit plasma_membrane and aligned</span>
            <span style="color: Green">%elseif MT.BoundPLM && ~MT.Growing  % hit plasma_membrane and NOT aligned</span>
            <span style="color: Green">%end</span>
            <span style="color: Green">%if  MT.BoundMic && MT.Growing  % hit another microtubule and aligned</span>
            <span style="color: Green">%elseif MT.BoundMic && ~MT.Growing  % hit another microtubule and NOT aligned</span>
            <span style="color: Green">%end</span>
            <span style="color: Green">%if  MT.BoundVac && MT.Growing  % hit vacuole membrane and aligned</span>
            <span style="color: Green">%elseif MT.BoundVac && ~MT.Growing  % hit vacuole membrane and NOT aligned</span>
            <span style="color: Green">%end</span>
            <span style="color: Green">% Keep the following</span>
            <span style="color: Green">% Clear flags from collision detector</span>
            MT.BoundPLM=false;
            MT.BoundMic=false;
            MT.BoundVac=false;
            data.working.dyn.microtubules.Org(i_MT)=MT;
        end
    end
<span style="color: Green">% put factors back into structure</span>
    for i=1:size( data.factorprops.Concentration,2)
        factname=lower(data.factorprops.Index2Name{i});
        eval(['data.factorprops.Concentration(:,i)=',[factname,'_p(:);']]);
    end   
end
<span style="color: Green">% This space intentionally left blank.</span>
<span style="color: Green">% Default factor parameters</span>
<span style="color: Green">% Default organelle parameters</span>
<span style="color: Green">%      cell_wall.size          =0.000000</span>
<span style="color: Green">%      cell_wall.offset        =0.500000</span>
<span style="color: Green">%      cell_wall.micronthick  =0.100000</span>
<span style="color: Green">%      cell_wall.minvox        =1.000000</span>
<span style="color: Green">%      cell_wall.FaceColor    =[1.000000,0.000000,1.000000,]</span>
<span style="color: Green">%      cell_wall.FaceAlpha    =0.010000</span>
<span style="color: Green">%      cell_wall.Label        =-5.000000</span>
<span style="color: Green">%      cell_wall.isLayer      =1.000000</span>
<span style="color: Green">%      cell_wall.Static        =1.000000</span>
<span style="color: Green">%      cell_wall.InUse        =1.000000</span>
<span style="color: Green">%plasma_membrane.size          =0.000000</span>
<span style="color: Green">%plasma_membrane.offset        =0.500000</span>
<span style="color: Green">%plasma_membrane.micronthick  =0.010000</span>
<span style="color: Green">%plasma_membrane.minvox        =3.000000</span>
<span style="color: Green">%plasma_membrane.FaceColor    =[1.000000,1.000000,0.000000,]</span>
<span style="color: Green">%plasma_membrane.FaceAlpha    =0.020000</span>
<span style="color: Green">%plasma_membrane.Label        =-4.000000</span>
<span style="color: Green">%plasma_membrane.isLayer      =1.000000</span>
<span style="color: Green">%plasma_membrane.Static        =1.000000</span>
<span style="color: Green">%plasma_membrane.InUse        =1.000000</span>
<span style="color: Green">%      cytoplasm.size          =0.000000</span>
<span style="color: Green">%      cytoplasm.offset        =0.500000</span>
<span style="color: Green">%      cytoplasm.micronthick  =1.000000</span>
<span style="color: Green">%      cytoplasm.minvox        =5.000000</span>
<span style="color: Green">%      cytoplasm.FaceColor    =[0.000000,1.000000,0.000000,]</span>
<span style="color: Green">%      cytoplasm.FaceAlpha    =0.020000</span>
<span style="color: Green">%      cytoplasm.Label        =0.000000</span>
<span style="color: Green">%      cytoplasm.isLayer      =1.000000</span>
<span style="color: Green">%      cytoplasm.Static        =1.000000</span>
<span style="color: Green">%      cytoplasm.InUse        =1.000000</span>
<span style="color: Green">%  microtubules.size          =0.025000</span>
<span style="color: Green">%  microtubules.minvoxel      =3.000000</span>
<span style="color: Green">%  microtubules.growthrate    =0.100000</span>
<span style="color: Green">%  microtubules.shrinkrate    =0.010000</span>
<span style="color: Green">%  microtubules.maxbend      =40.000000</span>
<span style="color: Green">%  microtubules.MaxAngle      =20.000000</span>
<span style="color: Green">%  microtubules.maxAge        =0.000000</span>
<span style="color: Green">%  microtubules.nuclspont    =0.050000</span>
<span style="color: Green">%  microtubules.nuclonMT      =0.090000</span>
<span style="color: Green">%  microtubules.probCatastrophe=0.300000</span>
<span style="color: Green">%  microtubules.FaceColor    =[0.000000,0.000000,1.000000,]</span>
<span style="color: Green">%  microtubules.FaceAlpha    =0.400000</span>
<span style="color: Green">%  microtubules.Label        =-6.000000</span>
<span style="color: Green">%  microtubules.isLayer      =0.000000</span>
<span style="color: Green">%  microtubules.Static        =0.000000</span>
<span style="color: Green">%  microtubules.InUse        =1.000000</span>
<span style="color: Green">%        vacuole.size          =0.200000</span>
<span style="color: Green">%        vacuole.offset        =0.500000</span>
<span style="color: Green">%        vacuole.micronthick  =1.000000</span>
<span style="color: Green">%        vacuole.minvox        =0.000000</span>
<span style="color: Green">%        vacuole.FaceColor    =[1.000000,1.000000,0.000000,]</span>
<span style="color: Green">%        vacuole.FaceAlpha    =0.300000</span>
<span style="color: Green">%        vacuole.Label        =-3.000000</span>
<span style="color: Green">%        vacuole.isLayer      =0.000000</span>
<span style="color: Green">%        vacuole.Static        =1.000000</span>
<span style="color: Green">%        vacuole.InUse        =1.000000</span>
<span style="color: Green">% Default cell parameters</span>
<span style="color: Green">% cellprops.shape          ='Rect:1:1:1'</span>
<span style="color: Green">% cellprops.sheetmodel    =0</span>
<span style="color: Green">% cellprops.maxLengthMicrons=10</span>
<span style="color: Green">% cellprops.secondsPerStep =1</span>
<span style="color: Green">% cellprops.micronsPerVoxelEdge=0.400000</span>
<span style="color: Green">% cellprops.cubicMicronsPerVoxel=0.064000</span>
<span style="color: Green">% cellprops.cellsize      =[25,25,25,]</span>
<span style="color: Green">% cellprops.colourType    =1</span>
<span style="color: Green">% cellprops.Vol            =[-1,-1,-1,-1, ... ]</span>
<span style="color: Green">% cellprops.Smooth        ='None'</span>
<span style="color: Green">% cellprops.dynamic        ='microtubules'</span>
<span style="color: Green">% cellprops.bound_distance =5</span>
<span style="color: Green">% cellprops.collide_distance=10</span>
<span style="color: Green">% cellprops.% vacuole.Vol=struct</span>
<span style="color: Green">% vacuole.EdgeVol=struct</span>
<span style="color: Green">% cellprops.% cell_wall.Vol=struct</span>
<span style="color: Green">% cell_wall.EdgeVol=struct</span>
<span style="color: Green">% cellprops.% plasma_membrane.Vol=struct</span>
<span style="color: Green">% plasma_membrane.EdgeVol=struct</span>
<span style="color: Green">% cellprops.% cytoplasm.Vol=struct</span>
<span style="color: Green">% cytoplasm.EdgeVol=struct</span>
<span style="color: Green">% cytoplasm.Indexes=struct</span>
<span style="color: Green">% cellprops.% Diameter.microtubules=struct</span>
<span style="color: Green">% cellprops.% microtubules.Vol=struct</span>
<span style="color: Green">% microtubules.Offsets=struct</span>
 
|}
|}
=Graphical User Interface=
=Graphical User Interface=

Revision as of 17:50, 1 May 2012

Return to Bangham Lab Software

Current Status

MTtbox is currently under test and further development
The main data structure is called: 'data'. It can be accessed from the Matlab command line by declaring data to be global. 

global data

at any time. The following documentation will refer to fields in data. It also refers to the custom menu items by menu:name.

First view of the MTtbox

1 A

The toolbox is launched with the command 
MTtbox

Which will cause the interface to appear at the top left of the monitor.
The left panel (accessed through the handle: data.PanelH) provides control and the right panel (data.plotprops.AxesH) displays the output. They can be dragged anywhere and returned to the top-left using menu:View:Controls to top-left.

 MTtbox GUI

1 B

A default project is created by selecting: menu:File:New Project

It forms a cell bounded by regions labelled: Outside, cell_wall, plasma_membrane, cytoplasm and vacuole. These are concentric volumes. Length is measured in microns (time in seconds). The axis labels indicate the thickness of each layer in terms of voxels in this particular model. This is extremely low resolution - it means that the microtubules will have to be unrealistically large. This is convenient for debugging and illustrating the system but not for simulations. The outer surface of each region is coloured, e.g. (Fig. on right) the vacuole is yellow and the cytoplasm is pale green.

The cell can be rotated etc. using the panels at the top of the display panel. Fig. below: all the regions have been hidden (uncheck each item in menu:View) and the mesh associated with the cytoplasm outer surface is displayed (check menu:View:Organelle meshes)
MTtbox GUI

MTtbox GUI

1 C

A project is saved by selecting: menu:File:Save as

Having first saved a project a default Interaction Function is created by selecting Edit. A default project file contains lots of comments to provide help on how to develop the project.

At present the Interaction Functions is not copied to the new project on each Save as command - this has to be done manually. 		(Comments are in green - this web version of the matlab file is created using webify_interaction_function('MT_Edinb_20120427.m')).

The default file is largely a copy of MTtbox_BoilerPlate.txt which should be updated to reflect the latest ideas on how to build the function.

Initial MTtbox interaction function is shown here

Graphical User Interface

2 A Changing organelles in the cell

menu:Organelles shows a list of organelles, check those that are required and then re-establish the working volumes (used for collision detection) by using menu:Prefs:Cell size and shape

2 B Changing working volumes used for collision detection

Current data structures

menu:Prefs:Cell size and shape establishes the shape of the cell and the arrangement of static organelles. The data structure it creates underpins the collision detection system. 
data.cellprops.Vol

is a volume filled with labels (range 0 to -7) representing regions: not-cell, cell-wall, plasma-membrane, cytoplasm, vacuole, etc. It is re-formed whenever the cell is redefined with pushbutton Initialise.

data.working.Vol

is a copy of data.cellprops.Vol which also contains regions representing dynamic organelles (microtubules and actin). It is re-zeroed by Restart. There are further volumes that supplement these two that are used for collision detection. Individual microtubule regions are recorded in 

data.cellprops.microtubules.Vol

each microtubule region is represented by a unique ID. Factors and their associated diffusion constants are represented by 

data.factorprops.Concentration
data.factorprops.DiffusionConst

each column of which represents a factor - they must be reshaped to the same format as the volume data.

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