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(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]) | (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 (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]. <br>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.]; | |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]. <br>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.]; | ||
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==<span style="color:DarkGreen;">VolViewer== | ==<span style="color:DarkGreen;">VolViewer== | ||
{| border="0" cellpadding="5" cellspacing="5" | {| border="0" cellpadding="5" cellspacing="5" | ||
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=<span style="color:DarkGreen;">Open source systems to which we contribute= | |||
==<span style="color:DarkGreen;">OMERO== | |||
{| border="0" cellpadding="5" cellspacing="5" | {| border="0" cellpadding="5" cellspacing="5" | ||
|- valign="top" | |- valign="top" | ||
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon> | |width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon> | ||
|width="40%"| | |width="40%"|For working with the OME image database. <br><br>See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download'']<br><br> | ||
For working with the OME image database. | (Windows, Mac, Linux) | ||
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. | |width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. | ||
|} | |} | ||
=<span style="color:DarkGreen;">Tools and Utilities= | |||
==<span style="color:DarkGreen;">BioformatsConverter== | |||
{| border="0" cellpadding="5" cellspacing="5" | {| border="0" cellpadding="5" cellspacing="5" | ||
|- valign="top" | |- valign="top" | ||
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon> | |width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon> | ||
|width="40%"| | |width="40%"|For converting microscope manufacturer proprietary file formats. <br><br>See [[BioformatsConverter|''Details'']], [[BioformatsConverter|''Download'']]<br><br> | ||
For converting microscope manufacturer proprietary file formats. <br>[[BioformatsConverter|''Details'']] | (Windows, Mac, Linux) | ||
|width="50%"| | |width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library. | ||
|} | |} | ||
Revision as of 11:55, 27 May 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.; |
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 (OMERO). |
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. |
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. |