Main Page

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. Details: what? How? Where? Tutorials: from the beginning Examples: from publications Download from SourceForge Ready Reference Manual (PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed Matlab 30 day free trial and student edition) Comment on results. R. Grant (2011) 'Taking Shape' TheScientist, 25:18

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 with 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. 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).