back to Vize lab home

Bioinformatics

 

 

We are exploring methods to store, transmit and display complex 4D gene expression data. An example of a scaffold model of a developing frog eye is shown on the right. It is live- try selecting a control and then click and drag on the eye. Models such as these will be used to display where different genes are active. More importantly it is hoped that such frameworks may allow computational analysis of transcription patterns and provide a powerful approach to identifying potential gene function.

Our group also runs the Xenopus model organism database, Xenbase. This DB integrates developmental and genomic data on frog development. It is presently a DB2 implementation running on Solaris.

Examples

 

Visit the Xenopus database front end

 

Key references:

Gerth, V.E. and Vize, P.D. (2004). A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns. Bioinformatics, (see PubMed).

Vize, P.D. (2004). Internet tools for cell and developmental biologists. In "The Internet for Molecular Biologists", R.Horton and C. Sansom Eds. The Practical Approach Series, Oxford University Press. ISBN 0199638888

Bowes, J.B. and Vize, P.D. (2003). Xenopus informatics. Current Genomics 4: 653-664.

Vize, P.D. (2001). On-line analysis of development. Bioessays, 23: 549-554

 

 

 

width=400 height=300> Java is currently not available on your browser. Please enable Java or upgrade to the latest version of a cool browser to view the model. Avoid all microsoft junk on principle.

model copyright © V. Gerth and P. Vize, 2002.

this model of a frog eye is live. click and drag or play with the controls- my fave is the measure tool. after selecting this tool click and drag your cursor over the model to measure distance between any two points (in microns).