MTtbox documentation: Difference between revisions

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[[Software#MTtbox|Return to Bangham Lab Software]]<br><br>
[[Software#MTtbox|Return to Bangham Lab Software]]<br><br>
=Why?=
The aim is to model the growth of microtubules (and other dynamic organelles such as actin). Organelles grow through chemical reactions and growing organelles can collide with other organelles and membranes. <br><br>
=How?=
To address these two features we adopted a data structure that stores microtubules as a list of vertices each of which is associated with a geometrically specified volume. Cell volumes are represented by a three dimensional array (lattice) of voxels. Regions within this volume are designated by numerical labels, e.g. 0 for cytoplasm, -4 for plasma-membrane. The size of the entire volume determines the resolution of the chemical reaction/diffusion system. Resolution increases with the number of voxels. Increasing the number of voxels decreases the speed of computation and increases the demand for memory (>=16 Gbytes memory is highly desirable). Dynamic organelles, such as microtubules, are represented as geometrical objects: tubes with hemispheric ends. These can collide with other microtubules, organelles and membranes. The most CPU time consuming step is collision detection.
==Current Status==
==Current Status==
MTtbox is currently under test and further development<br>
MTtbox is currently under test and further development<br>
The main data structure is called: 'data'. It can be accessed from the Matlab command line by declaring data to be global.
[http://rico-coen.jic.ac.uk/LabGuide/index.php/Modelling_using_MTtbox Pre-release internal documentation]
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.
<br>
=Graphical User Interface=
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="300pt"|The toolbox is launched with the command
MTtbox
Which will cause the interface to appear at the top left of the monitor.<br>
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.<br><br>
 
|width="700pt"|[[Image:MTtboxUserInterface.png|700px|MTtbox GUI]]
|}
===1 B===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="500pt"|A default project is created by selecting: ''menu:File:New Project''<br><br>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.<br><br>
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'')<br>
[[Image:MTtboxCytoplasmMesh.png|300px|MTtbox GUI]]
|width="400pt"|[[Image:MTtboxDefaultProject.png|400px|MTtbox GUI]]
|}
===1 C===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="500pt"|A project is saved by selecting: ''menu:File:Save as''<br><br>Having first saved a project a default Interaction Function is created by selecting ''Edit''. A default project file [[MTtbox default interaction function|(example of the default interaction function)]] contains lots of comments to provide help on how to develop the project.<br><br>At present the Interaction Functions is not copied to the new project on each Save as command - this has to be done manually.
|width="400pt"|[[Image:MTtboxDefaultProject.png|400px|MTtbox GUI]]
|}

Latest revision as of 12:11, 11 December 2012

Return to Bangham Lab Software

Why?

The aim is to model the growth of microtubules (and other dynamic organelles such as actin). Organelles grow through chemical reactions and growing organelles can collide with other organelles and membranes.

How?

To address these two features we adopted a data structure that stores microtubules as a list of vertices each of which is associated with a geometrically specified volume. Cell volumes are represented by a three dimensional array (lattice) of voxels. Regions within this volume are designated by numerical labels, e.g. 0 for cytoplasm, -4 for plasma-membrane. The size of the entire volume determines the resolution of the chemical reaction/diffusion system. Resolution increases with the number of voxels. Increasing the number of voxels decreases the speed of computation and increases the demand for memory (>=16 Gbytes memory is highly desirable). Dynamic organelles, such as microtubules, are represented as geometrical objects: tubes with hemispheric ends. These can collide with other microtubules, organelles and membranes. The most CPU time consuming step is collision detection.

Current Status

MTtbox is currently under test and further development
Pre-release internal documentation

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