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First home page - Revision history
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AndrewBangham: Created page with '__NOTOC__ {| border="0" cellpadding="0" cellspacing="0" |- valign="top" |width="50%"|<span style="color: DarkSlateGray"><font size="+1">'''The Bangham Lab'''</font><span> || ||'…'
2011-05-31T06:47:07Z
<p>Created page with '__NOTOC__ {| border="0" cellpadding="0" cellspacing="0" |- valign="top" |width="50%"|<span style="color: DarkSlateGray"><font size="+1">'''The Bangham Lab'''</font><span> || ||'…'</p>
<p><b>New page</b></p><div>__NOTOC__<br />
{| border="0" cellpadding="0" cellspacing="0" <br />
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|width="50%"|<span style="color: DarkSlateGray"><font size="+1">'''The Bangham Lab'''</font><span><br />
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||'''Contents'''<br />
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|width="100pt"|[[Main_Page#Computational Biology|'''GFtbox''']] <br />
|width="100pt"| [[GFtbox|Details]] <br />
|width="100pt"| [https://sourceforge.net/p/gftbox/ Download ]<br />
|width="100pt"| [[GFtbox Tutorial pages|Tutorials]] <br />
|-<br />
|width="100pt"|[[Main_Page#Computational Biology|'''VolViewer''' ]] <br />
|width="100pt"| [[VolViewer|Details]] <br />
|width="100pt"| [[VolViewer|Download]] <br />
|width="100pt"| [[VolViewerUserManual|Manual]] <br />
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|width="100pt"|[[Main_Page#Photos and Art|'''Art''']]<br />
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|width="100pt"|[[Main_Page#Algorithms, Tools and Demonstrations|'''Algorithms''']]<br />
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=<span style="color: DarkGreen">Computational Biology</span>=<br />
<span style="color: DarkGreen"><font size="+1">The aim </font><span>is to understand how patterns of gene activity in biological organs influence the developing shape. </span><p></p><p></p><br />
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LabelledCropped_GPT_Snapdragon_2010-000250-0001.png<br />
LabelledCropped_GPT_Snapdragon_2010-000340-0001.png<br />
LabelledCropped_GPT_Snapdragon_2010-000490-0001.png<br />
LabelledCropped_GPT_Snapdragon_2010-000570-0002.png<br />
LabelledCropped_GPT_Snapdragon_2010-000570-0003.png<br />
LabelledCropped_GPT_Snapdragon_2010-000570-0004.png<br />
LabelledCropped_GPT_Snapdragon_2010-000570-0005.png<br />
LabelledCropped_GPT_Snapdragon_2010-000570-0007.png<br />
LabelledCropped_GPT_Snapdragon_2010-000570-0006.png<br />
LabelledCropped_GPT_Snapdragon_2010-000570-0001.png<br />
</sgallery><br />
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More Snapdragon model</span>]] </center><br />
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=<span style="color: Gold">Genes and growing shapes (modelling)</span>= <br />
* <span style="color: LemonChiffon">Observation: patterns of gene activity that regulate tissue growth.</span><br />
* <span style="color: LemonChiffon">Hypothesis: gene activity independently regulates direction of growth.</span><br />
* <span style="color: LemonChiffon">Formalised in the Growing Polarised Tissue Framework (cite). </span><br />
* <span style="color: LemonChiffon">Implemented in ''GFtbox'' (cite) for developing ideas on growth and form.</span><br />
** <span style="color: LemonChiffon">Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity (cite). </span><br />
** <span style="color: LemonChiffon">Grow the canvas in 3D under constraints of tissue continuity</span><br />
** <span style="color: LemonChiffon">Compare with observed data quantitatively(cite). </span><p><br />
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Download and more details on ''GFtbox''</span>]] </center><br />
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LabelledCropped GPT Snapdragon 2010-000570-0003 double.png<br />
LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png<br />
LabelledCropped GPT Snapdragon 2010-000570-0001-Wildtype.png<br />
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<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on testing models</span>]] </center><br />
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Arabidopsis_Leaf_ATH8bbg.png<br />
Antirrhinum flower small1.jpg<br />
Antirrhinum flower small2.jpg<br />
Antirrhinum flower small3.jpg<br />
Anthers1.jpg<br />
MacroOPTIris1.jpg<br />
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<center> [[VolViewer|<span style="color:GreenYellow;">More on visualising 3D</span>]] </center><br />
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=<span style="color: Gold">Viewing 3D volume images (analysis)<span>= <br />
*<span style="color: LemonChiffon">Three dimensional (3D) volume images are key to understanding the development of shape. </span><br />
* <span style="color: LemonChiffon">Produced by</span><br />
** <span style="color: LemonChiffon">CT X-ray scanners, MRI and PET.</span><br />
** <span style="color: LemonChiffon">Confocal microscopy and OPT (ref) used with fluorescent probes that monitor biological gene activity. </span><br />
** <span style="color: LemonChiffon">Huge amounts of data potentially make viewing slow, but...</span><br />
* <span style="color: LemonChiffon">To interact with the images we implemented '''VolViewer''' (cite) which exploits powerful graphics processors.</span><br />
* <span style="color: LemonChiffon">Works with [[Software#Toolboxes for research|<span style="color:GreenYellow;">BioformatsConverter</span>]] to read 3D images in both open and proprietary file formats. Runs on either your computer or a server.</span> <br />
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Download and more details on ''VolViewer''</span>]] </center><br />
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Arabidopsis_Leaf_ATH8bbg.png<br />
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<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on 3D measurement</span>]] </center><br />
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=Photos and Art=<br />
=Algorithms, Tools and Demonstrations=<br />
=About=<br />
<span style="color:DarkSlateGray;">The Bangham Lab is part of the [http://www.uea.ac.uk/cmp/research/cmpbio| <span style="color:SlateGray;">UEA D’Arcy Thompson Centre] for computational biology and it's members collaborate closely with [http://rico-coen.jic.ac.uk/index.php/Main_Page|<span style="color:SlateGray;">the Coen Lab, John Innes Centre</span>]<br />
<br />
==<span style="color:DarkSlateGray;">Updated [[User:AndrewBangham|Andrew Bangham]] 09:50, 4 May 2011 (UTC)==</div>
AndrewBangham