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(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> | (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> | ||
Comment on results. [http://www.the-scientist.com/2011/4/1/18/1/ R. Grant (2011) 'Taking Shape' TheScientist, 25:18] | Comment on results. [http://www.the-scientist.com/2011/4/1/18/1/ R. Grant (2011) 'Taking Shape' TheScientist, 25:18] | ||
|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 | |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. | ||
A paper describing the method and the software has appeared in [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== | ||
Revision as of 15:26, 21 July 2011
Bangham Lab - Home
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.
A paper describing the method and the software has appeared in PLoS Computational Biology. |
VolViewer
| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon> | For viewing and measuring biological images. Details (Windows, Mac, Linux) |
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). |