Gel2DE

Gel2DE is an application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake.

Download and install

To download a binary version of the software together with a user manual, click the "Downloads" tab above and download the latest .zip file (only available for Windows)

Getting started

To get started with the application, run the gelcorrelation.exe from the downloaded .zip file. To open the bundled test dataset, go to the "File" -> "Open" and open exampledata\project.xml. This should load the synthetic dataset. Use the two middle sliders to adjust contrast and brightness in the gel images. Select a parameter (for instance 'Age') and press Calculate corr. This will generate a correlation image. Below the correlation image, use the drop down box menu to select different visualizations, for instance C*S*D, which is the correlation weighted by the standard deviation and significance. See the .PDF user manual in the downloaded .zip file for more information.

Test synthetic data set

The application is bundled with a synthetic test dataset, the same that is used in Van Belle et al 2006 (see References below).

Compilation from source

Check out the source code from svn as described under the "Source" tab. Read the README.txt for instructions.

References

The reference for this application is:

Ola Kristoffer Øye, Katarina M. Jørgensen, Sigrun M. Hjelle, André Sulen, Dag Magne Ulvang, Bjørn Tore Gjertsen: Gel2DE - A software tool for correlation analysis of 2D gel electrophoresis data, BMC Bioinformatics 2013, 14:215, doi:10.1186/1471-2105-14-215

http://www.biomedcentral.com/1471-2105/14/215

The application implements the methodology proposed in:

Werner Van Belle, Nina Ånensen, Ingvild Haaland, Øystein Bruserud, Kjell-Arild Høgda and Bjørn Tore Gjertsen: Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables, BMC Bioinformatics 2006, 7:198 doi:10.1186/1471-2105-7-198

http://www.biomedcentral.com/1471-2105/7/198