The Open2Dprot Project

Description:
The Open2Dprot project is a community effort to create an open source 2D protein expression data analysis system to investigate and find signficant protein expression profiles relevant to the experiments. When it becomes available, it will be downloadable and could be used for data mining protein expression across sets of 2D data from research experiments. In the initial development phase, modules will be created for 2D-dimensional data including 2D-PAGE (polyacrylamide gel electrophoresis) and initial support for 2D LC-MS and other data. In the second phase, it will be expanded to handle data from other 2D protein separation methods. It will initially implement a minimal analysis system including the ability to sequentially analyze data by:

• Accessioning (i.e., enter) scanned sample images and experiment information into a user's experiment project database
• Creating a landmark database between reference sample and remaining samples by spot pairing algorithm (if spot pairing is not automatic)
• Pairing "spots" between a reference sample and the rest of samples
• Constructing a composite sample database from this data for subsequent exploratory data analysis
• Exploring the database using exploratory data analysis techniques: statistics, clustering, direct-manipulation graphics and reports, etc. including access to various Internet proteomic databases.
• Quantify polypeptide "spots" by image processing of 2D gel images or cluster polypeptide assembled "spots" by clustering a series of 2D LC-MS, protein arrays, or other separation methods.

Web Sites:
http://open2dprot.sourceforce.net/
http://www.ccrnp.ncifcrf.gov/Open2Dprot


Availability:
Open-source, downloadable (to be released 2004)

Cost:
Free

Contact:
Dr. Peter Lemkin; lemkin@ncifcrf.gov

This page last updated 2006-09-05 15:58:01