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|width="50%"|<span style="color: DarkSlateGray"><font size="+1">'''The Bangham Lab'''</font><span>
|width="50%"|<span style="color: DarkSlateGray"><font size="+1">'''The Bangham Lab'''</font><span>
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|width="100pt"|'''Growth'''                   
|width="100pt"|[[Main_Page#Computational Biology|'''GFtbox''']]                    
|width="100pt"|'''3D Viewer'''                     
|width="100pt"| [[GFtbox|Details]] 
|width="100pt"|'''Shapes'''
|width="100pt"| [https://sourceforge.net/p/gftbox/ Download ]
|width="100pt"|'''Art'''
|width="100pt"| [[GFtbox|Manual]]
|width="100pt"|'''Algorithms'''
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|width="100pt"| [[GFtbox|Details]]  
|width="100pt"|[[Main_Page#Computational Biology|'''VolViewer''' ]]                    
|width="100pt"| [[VolViewer|Details]]  
|width="100pt"| [[VolViewer|Details]]  
|width="100pt"|  [[VolViewer|Download]]
|width="100pt"| [[VolViewerUserManual|Manual]]
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|width="100pt"|[[Main_Page#Computational Biology|'''Shapes''']]
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|width="100pt"| [[https://sourceforge.net/p/gftbox/ Download ]]
|width="100pt"|[[Main_Page#Photos and Art|'''Art''']]
|width="100pt"|  [[VolViewer|Download]]  
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|width="100pt"| [[GFtbox|Manual]]
|width="100pt"|[[Main_Page#Algorithms, Tools and Demonstrations|'''Algorithms''']]
|width="100pt"| [[VolViewerUserManual|Manual]]  
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<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More Snapdragon model</span>]] </center>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More Snapdragon model</span>]] </center>
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=<span style="color: Gold">Genes and growing shapes</span>=  
=<span style="color: Gold">Genes and growing shapes (modelling)</span>=  
* <span style="color: LemonChiffon">Observed: patterns of gene activity regulate tissue growth.</span>
* <span style="color: LemonChiffon">Observed: patterns of gene activity regulate tissue growth.</span>
* <span style="color: LemonChiffon">Hypothesis: gene activity independently regulates direction of growth.</span>
* <span style="color: LemonChiffon">Hypothesis: gene activity independently regulates direction of growth.</span>
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<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on visualising 3D</span>]] </center>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on visualising 3D</span>]] </center>
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=<span style="color: Gold">Working with 3D volume images<span>=  
=<span style="color: Gold">Viewing 3D volume images (analysis)<span>=  
*<span style="color: LemonChiffon">Three dimensional (3D) volume images are key to understanding the development of shape. </span>
*<span style="color: LemonChiffon">Three dimensional (3D) volume images are key to understanding the development of shape. </span>
* <span style="color: LemonChiffon">Produced by</span>
* <span style="color: LemonChiffon">Produced by</span>

Revision as of 17:06, 4 May 2011

The Bangham Lab Contents: quick-links
GFtbox Details Download Manual
VolViewer Details Download Manual
Shapes 5 6 7
Art 5 6 7
Algorithms 5 6 7

Computational Biology

The aim is to understand how patterns of gene activity in biological organs influence the developing shape.

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="2000"> LabelledCropped_GPT_Snapdragon_2010-000250-0001.png LabelledCropped_GPT_Snapdragon_2010-000340-0001.png LabelledCropped_GPT_Snapdragon_2010-000490-0001.png LabelledCropped_GPT_Snapdragon_2010-000570-0002.png LabelledCropped_GPT_Snapdragon_2010-000570-0003.png LabelledCropped_GPT_Snapdragon_2010-000570-0004.png LabelledCropped_GPT_Snapdragon_2010-000570-0005.png LabelledCropped_GPT_Snapdragon_2010-000570-0007.png LabelledCropped_GPT_Snapdragon_2010-000570-0006.png LabelledCropped_GPT_Snapdragon_2010-000570-0001.png </sgallery>

More Snapdragon model

Genes and growing shapes (modelling)

  • Observed: patterns of gene activity regulate tissue growth.
  • Hypothesis: gene activity independently regulates direction of growth.
  • Formalised in the Growing Polarised Tissue Framework (cite).
  • Implemented in GFtbox (cite) for developing ideas on growth and form.
    • Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity.
    • Grow the canvas in 3D under constraints of tissue continuity
    • Compare with observed data quantitatively

Download and more details on GFtbox

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000"> LabelledCropped GPT Snapdragon 2010-000570-0003 double.png LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png LabelledCropped GPT Snapdragon 2010-000570-0001-Wildtype.png </sgallery>

More on testing models

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="1500"> Arabidopsis_Leaf_ATH8bbg.png Antirrhinum flower small1.jpg Antirrhinum flower small2.jpg Antirrhinum flower small3.jpg Anthers1.jpg MacroOPTIris1.jpg </sgallery>

More on visualising 3D

Viewing 3D volume images (analysis)

  • Three dimensional (3D) volume images are key to understanding the development of shape.
  • Produced by
    • CT X-ray scanners, MRI and PET.
    • Confocal microscopy and OPT (ref) used with fluorescent probes that monitor biological gene activity.
    • Huge amounts of data potentially make viewing slow, but...
  • To interact with the images we implemented VolViewer (cite) which exploits powerful graphics processors.
  • Works with BioformatsConverter to read 3D images in both open and proprietary file formats
Download and more details on VolViewer

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000"> Arabidopsis_Leaf_ATH8bbg.png </sgallery>

More on 3D measurement

Photos and Art

Algorithms, Tools and Demonstrations

About

The Bangham Lab is part of the UEA D’Arcy Thompson Centre for computational biology and it's members collaborate closely with the Coen Lab, John Innes Centre

Updated Andrew Bangham 09:50, 4 May 2011 (UTC)

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