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=<span style="color:DarkGreen;">Computational biology toolboxes= | =<span style="color:DarkGreen;">Computational biology toolboxes= | ||
==<span style="color:DarkGreen;">GFtbox== | ==<span style="color:DarkGreen;">GFtbox== | ||
{| border="0" cellpadding="5" cellspacing="5" | {| border="0" cellpadding="5" cellspacing="5" | ||
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|width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon> | |width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon> | ||
|width="40%"| | |width="40%"| | ||
For modelling the growth of shapes. <br><br> | For modelling the growth of shapes. <br><br> | ||
[[GFtbox|'''''Details''''']]<br><br> | |||
[[GFtbox Tutorial pages|'''''Tutorials''''']]<br><br> | |||
[https://sourceforge.net/p/gftbox/ '''''Download''''']<br><br> | |||
[[Ready Reference Manual|'''''Ready Reference Manual''''']]<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> | (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 (PLoS Computational Biology, ''in press''). <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]. | |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 (PLoS Computational Biology, ''in press''). <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 new mutant 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 direction organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by the interaction of a background polariser that forms a gradient along the mesh and a source of polariser generated by an organiser that comes to be the tip of the outgrowth. | ||
|} | |} | ||
==<span style="color:DarkGreen;">VolViewer== | ==<span style="color:DarkGreen;">VolViewer== | ||
Revision as of 09:43, 2 June 2011
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, in press). 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 new mutant 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 direction organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by the interaction of a background polariser that forms a gradient along the mesh and a source of polariser generated by an organiser that comes to be the tip of the outgrowth. |
VolViewer
| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon> | For viewing and measuring 3D volume images. See Details, Download (Windows, Mac, Linux) |
VolViewer makes extensive use of OpenGL and Qt. It is open-source and is compatible with the Open Microscopy Environment (OME). |
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 (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, Download (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. |