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The Bangham Lab

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 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 Downloads 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	Working with 3D volume images 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 (cite) used with fluorescent probes that monitor biological gene activity. Huge amounts of data potentially make viewing slow, but... Implemented VolViewer (cite) which exploits powerful graphics processors. Works with BioformatsConverter to read open and proprietary file formats Downloads 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

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Algorithms, Tools and Demonstrations

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The Bangham Lab is part of the UEA D’Arcy Thompson Centre<!span> for computational biology and collaborates closely with [the Coen Lab, John Innes Centre] --Andrew 09:50, 4 May 2011 (UTC)