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__NOTOC__
__NOTOC__
{| border="0" cellpadding="0" cellspacing="0"  
=<span style="color:IndianRed;">'''Current'''=
=<span style="color:DarkGreen;">Computational biology toolboxes=
==<span style="color:DarkGreen;">GFtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|- valign="top"
|width="50%"|<span style="color: DarkSlateGray"><font size="+1">'''The Bangham Lab'''</font><span>
|width="10%"| <imgicon>GPT_thumbnail.png|120px|GFtbox</imgicon>
||
|width="40%"|
||'''Contents'''
For modelling the growth of shapes.  <br><br>See [[GFtbox|''Details'']], [[GFtbox Tutorial pages|''Tutorials'']] and [https://sourceforge.net/p/gftbox/ ''Download'']<br><br>
(PC, Mac, Linux, uses Matlab<br>[http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and <br>[http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition])
|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos.
|}
==<span style="color:DarkGreen;">VolViewer==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|- valign="top"
|width="50%"|
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>  
|||<center><small>
|width="40%"|For viewing and measuring 3D volume images. <br><br>See [[VolViewer|''Details'']], [[VolViewer|''Download'']]<br><br>
{| border="0" cellpadding="0" cellspacing="0"
(PC: Windows, your computer or a server)
|width="100pt"|[[Main_Page#Computational Biology|'''GFtbox''']]                  
|width="50%"|  VolViewer makes extensive use of [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt]. It is open-source and forms a part of the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
|width="100pt"| [[GFtbox|Details]] 
|width="100pt"| [https://sourceforge.net/p/gftbox/ Download ]
|width="100pt"| [[GFtbox Tutorial pages|Tutorials]]
|-
|width="100pt"|[[Main_Page#Computational Biology|'''VolViewer''' ]]                    
|width="100pt"| [[VolViewer|Details]]
|width="100pt"|  [[VolViewer|Download]]
|width="100pt"| [[VolViewerUserManual|Manual]]
<!--|-
|width="100pt"|[[Main_Page#Computational Biology|'''Shapes''']]
|width="100pt"| 5
|width="100pt"| 6
|width="100pt"| 7
|-
|width="100pt"|[[Main_Page#Photos and Art|'''Art''']]
|width="100pt"| 5
|width="100pt"| 6
|width="100pt"| 7
|-
|width="100pt"|[[Main_Page#Algorithms, Tools and Demonstrations|'''Algorithms''']]
|width="100pt"| 5
|width="100pt"| 6
|width="100pt"| 7 -->
|}
|}
</small></center>
 
==<span style="color:DarkGreen;">Computational biology systems to which we contribute==
===<span style="color:DarkGreen;">BioformatsConverter===
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"| (PC: Windows)
For converting microscope manufacturer proprietary file formats. <br>[[BioformatsConverter|''Details'']]<br>''Download''
|width="50%"|  This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard.
|}
|}
 
===<span style="color:DarkGreen;">OMERO===
=<span style="color: DarkGreen">Computational Biology</span>=
{| border="0" cellpadding="5" cellspacing="5"
<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>
|- valign="top"
{| border="0" cellpadding="5" cellspacing="3"  style="background-color: #000000;"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>  
| <!-- column1-->
|width="40%"| (web client - SQL server)
<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="2000">
For working with the OME image database. <br>''Details''<br>''Download''
LabelledCropped_GPT_Snapdragon_2010-000250-0001.png
|width="50%"|   [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data.
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>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More Snapdragon model</span>]] </center>
|| <!-- column2-->
=<span style="color: Gold">Genes and growing shapes (modelling)</span>=
* <span style="color: LemonChiffon">Observation: patterns of gene activity that regulate tissue growth.</span>
* <span style="color: LemonChiffon">Hypothesis: gene activity independently regulates direction of growth.</span>
* <span style="color: LemonChiffon">Formalised in the Growing Polarised Tissue Framework (cite). </span>
* <span style="color: LemonChiffon">Implemented in ''GFtbox'' (cite) for developing ideas on growth and form.</span>
** <span style="color: LemonChiffon">Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity (cite). </span>
** <span style="color: LemonChiffon">Grow the canvas in 3D under constraints of tissue continuity</span>
** <span style="color: LemonChiffon">Compare with observed data quantitatively(cite). </span><p>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Download and more details on ''GFtbox''</span>]] </center>
||  <!-- column3-->
<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
<!--Arabidopsis_Leaf_ATH8bbg.png-->
<!--Grandison-Simulation.png-->
<!--PaulProjectPic.png-->
<!--Pierre_project_image.jpg-->
</sgallery>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on testing models</span>]] </center>
|-  <!-- row2-->
|
<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
<!--Grandison-Simulation.png-->
<!--PaulProjectPic.png-->
<!--Pierre_project_image.jpg-->
</sgallery>
<center> [[VolViewer|<span style="color:GreenYellow;">More on visualising 3D</span>]] </center>
|| <!-- column2-->
=<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">Produced by</span>
** <span style="color: LemonChiffon">CT X-ray scanners, MRI and PET.</span>
** <span style="color: LemonChiffon">Confocal microscopy and OPT (ref) used with fluorescent probes that monitor biological gene activity. </span>
** <span style="color: LemonChiffon">Huge amounts of data potentially make viewing slow, but...</span>
* <span style="color: LemonChiffon">To interact with the images we implemented '''VolViewer''' (cite) which exploits powerful graphics processors.</span>
* <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>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Download and more details on ''VolViewer''</span>]] </center>
|| <!-- column3-->
<sgallery width="140" height="200"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
Arabidopsis_Leaf_ATH8bbg.png
<!--Grandison-Simulation.png-->
<!--PaulProjectPic.png-->
<!--Pierre_project_image.jpg-->
</sgallery>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on 3D measurement</span>]] </center>
|-  <!-- row3-->
|  <!-- column1-->
|| <!-- column2-->
|| <!-- column3-->
|}
|}


=Photos and Art=
=Algorithms, Tools and Demonstrations=
=About=
<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>]


==<span style="color:DarkSlateGray;">Updated [[User:AndrewBangham|Andrew Bangham]] 09:50, 4 May 2011 (UTC)==
=Algorithms, demonstrations and tools=

Revision as of 09:31, 26 May 2011

Current

Computational biology toolboxes

GFtbox

<imgicon>GPT_thumbnail.png|120px|GFtbox</imgicon>

For modelling the growth of shapes.

See Details, Tutorials and Download

(PC, Mac, Linux, uses Matlab
Matlab 30 day free trial and
student edition)

GFtbox is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos.

VolViewer

<imgicon>VolViewer-logo.png|120px|VolViewer</imgicon> For viewing and measuring 3D volume images.

See Details, Download

(PC: Windows, your computer or a server)

VolViewer makes extensive use of OpenGL and Qt. It is open-source and forms a part of the Open Microscopy Environment (OME).

Computational biology systems to which we contribute

BioformatsConverter

<imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon> (PC: Windows)

For converting microscope manufacturer proprietary file formats.
Details
Download

This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard.

OMERO

<imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon> (web client - SQL server)

For working with the OME image database.
Details
Download

Open Microscopy Environment Remote Objects (OMERO). for visualising, managing, and annotating scientific image data.


Algorithms, demonstrations and tools

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