Biomedical Image Processing and Database Analysis Group

Our group is in the

Open2Dprot 2D protein expression data analysis, MAExplorer microarray expression analysis, Flicker image comparison, 2DWG meta-database of 2D gels, dbEngine simple database Web publishing, GELLAB-II 2D gel analysis

Peter Lemkin

Greg Thornwall

Quang Tri Nguyen (also in TOG/LCRC/NCI)

Information on the following IPS projects

• Microarray Explorer (MAExplorer) is an open source Java-based data-mining facility for cDNA or oligonucleiotide microarray databases. It may be downloaded from http://maexplorer.sourceforge.net and run as a stand-alone application on your computer. Its exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.

2D proteomics tools

• Open2Dprot, located at Open2Dprot.sourceforge.net, is a community effort to create an open source n-dimensional protein expression data analysis system. It will be downloadable and could be used for data mining protein expression across sets of n-D data from research experiments. In the initial phase, modules will be created for 2-D data including 2D-PAGE (polyacrylamide gel electrophoresis) and initial support for 2-D LC-MS and other data. In the second phase, it will be expanded to handle data from other n-dimensional protein separation methods such as LC-MS*MS*...*MS.

• The Flicker program has been contributed to the open source Open2Dprot project at http://open2dprot.sourceforge.net/Flicker. It lets researchers compare of images across the Internet (2D gel and other images. The new stand-alone downloadable Java Flicker program was derived from the old Flicker applet with many more capabilities including: better zoom, image contrast, image transforms, limited measurement quantification and grayscale calibration, links to SWISS-2DPAGE, etc.

• The Seg2Dgel program has been contributed to the open source Open2Dprot project at http://open2dprot.sourceforge.net/Seg2Dgel. It performs spot detection and quantification of 2D gel and other similar types of images. It is a stand-alone downloadable Java program that will be used as part of the Open2Dprot analysis pipeline.

• The CmpSpots program has been contributed to the open source Open2Dprot project at http://open2dprot.sourceforge.net/CmpSpots. It performs spot-pairing between 2D spot list of 2D data such as 2D PAGE gels, 2D LC-MS, and other protein separation sources. It is a stand-alone downloadable Java program that will be used as part of the Open2Dprot analysis pipeline.

• GELLAB-II software for two-dimensional electrophoretic gel analysis. GELLAB-II is no longer available, but the concepts are being used as part of the new Open2Dprot project.

2D protein gel databases

• Public-access 2D-gel image data sets are available for public use.
• 2DWG meta-database of 2D protein gel images found on the Internet

• Table of links to 2D gel Electrophoresis database servers on the Web

List of IPS Databases

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