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|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 ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 PLoS Computational Biology]). <br><br>The GPT-framework was used to capture an understanding of (to model) the [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 growing Snapdragon flower]. The Snapdragon model was validated by [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 comparing the results with other mutant and transgenic flowers.]<br><br>The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. | |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 ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 PLoS Computational Biology]). <br><br>The GPT-framework was used to capture an understanding of (to model) the [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 growing Snapdragon flower]. The Snapdragon model was validated by [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 comparing the results with other mutant and transgenic flowers.]<br><br>The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. | ||
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==<span style="color:DarkGreen;">VolViewer== | ==<span style="color:DarkGreen;">VolViewer== | ||
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==<span style="color:DarkGreen;">AAMToolbox== | |||
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|width="10%"| <imgicon>AAMToolbox-logo.png|120px|AAMToolbox</imgicon> | |||
|width="40%"|For analysing shapes using principal component analysis. <br><br> | |||
[[AAMToolbox Details|'''''Details''''': what? How? Where?]]<br><br> | |||
[[AAMToolbox Documentation|'''''Tutorials''''': from the beginning]]<br><br> | |||
[[AAMToolbox Download| '''''Download''''']]<br><br> | |||
(PC, Mac, Linux, uses Matlab<br>no Mathworks toolboxes needed<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])<br><br> | |||
|width="50%"| The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading, we have used it extensively for analysing the shapes of leaves and petals. We have also used it to analyse portraits by, for example, Leonardo de Vinci and Modigliani. | |||
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=<span style="color:DarkGreen;">Open source systems to which we contribute= | =<span style="color:DarkGreen;">Open source systems to which we contribute= | ||
==<span style="color:DarkGreen;">OMERO== | ==<span style="color:DarkGreen;">OMERO== | ||
Revision as of 21:28, 24 January 2012
Current activity: a collaboration with the CoenLab with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.
Computational biology toolboxes
GFtbox
| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon> |
For modelling the growth of shapes. |
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 (PLoS Computational Biology). The GPT-framework was used to capture an understanding of (to model) the growing Snapdragon flower. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers. The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. |
VolViewer
| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon> | For viewing and measuring biological images. Details: what? How? Where? |
VolViewer uses OpenGL and Qt to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment (OME). |
AAMToolbox
| <imgicon>AAMToolbox-logo.png|120px|AAMToolbox</imgicon> | For analysing shapes using principal component analysis. Details: what? How? Where? |
The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading, we have used it extensively for analysing the shapes of leaves and petals. We have also used it to analyse portraits by, for example, Leonardo de Vinci and Modigliani. |
Open source systems to which we contribute
OMERO
| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon> | For working with the OME image database. See Details, Download OMERO Workshop (Windows, Mac, Linux) |
Open Microscopy Environment Remote Objects (OMERO). for visualising, managing, and annotating scientific image data. See also our OMERO Workshop training course we ran in April 2011. |
Tools and Utilities
BioformatsConverter
| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon> | For converting microscope manufacturer proprietary file formats. See Details (Windows, Mac, Linux) |
This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the Bioformats library. |