BanghamLabSVN
DArT_Toolshed
The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 A Multiscale Approach to Genes Growth and Geometry (a collaboration with the CoenLab). A 0.6 MB zipped copy (21st May 2013) is available DArT_Toolbox_Download.zip Revision 4699
Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively.
Why Matlab? The language suits our problems. For example, GFtbox - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, A and B. We might make the hypothesis that the growth rate is specified by A but partially inhibited by B (inhibited by an amount K). This is a simple idea that can be expressed in Matlab equally simply by writing Growth=A .* inh(K, B). This is because variables A and B can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (inh). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model.
Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors.
Toolboxes: File level help
Total 2828 functions.
Algorithms: File level help
Total 252 functions.
Attachments: File level help
Total 107 functions.
IOMethods: File level help
Total 4 functions.
ToolBag: File level help
Total 185 functions.