Research Newsletter

Informatics professor to lead proteomics research team

Using high-speed computer networks and Indiana University's supercomputer, a team of researchers from IU and Purdue University will be contributing to an open-source bioinformatics software platform development project in proteomics (the study of the structure and function of proteins), thanks to a $25,000 bioinformatics research award from the Canary Foundation. The San Jose, California-based foundation's slogan is "stopping cancer early", and it awards funding for cancer-related research to accelerate realization of that goal.

Canary, and the LabKey Software Foundation designated five grant recipients from around the world for their Bioinformatics Platform Dissemination Award, and among the 50 contenders was the Indiana bioinformatics group, led by Dr. Jake Y. Chen, assistant professor of informatics and computer science, IU School of Informatics at IUPUI. Dr. Chen is also a member of the IU Simon Cancer Center Experimental and Developmental Therapeutics Program.

The awarded research teams nationwide will share $225,000 in total funding to be used to customize and expand CPAS (Computational Proteomics Analysis System), an open source proteomics data analysis and data management platform. CPAS is based on LabKey Server and includes a large number of proteomics data processing tools.

"We'll be using the state of Indiana's I-Light high-speed data network, the IU supercomputer "Big Red", and IU's mass data storage systems on the Bloomington and Indianapolis campuses to enable co-development and operation of the CPAS proteomics software pipeline at both Indiana University and Purdue University computational proteomics facility sites," said Dr. Chen.

Prof. Chen's team will install and custom-develop CPAS software for local Central Indiana proteomics users. Co-PI of the award is Dr. Xiang Zhang, principle bioinformatics scientist at Bindley Bioscience Center, Purdue University, West Lafayette. Rounding out the team are senior investigator Stephen Simms, manager, Data Capacitor project, IU Bloomington; and senior investigator Kurt Seiffert, Distributed Storage Services Group, IUPUI.

"Our work will make significant steps toward the Canary Foundation's eventual goal of developing reliable methods for early cancer detection and intervention," said Simms. "The Data Capacitor is a unique resource that empowers collaborative research. It can be accessed by multiple resources across distance, and will enable data sharing and workflow opportunities that were previously cumbersome or in some cases impossible," he added.

"Funding for the CPAS deployment can help us launch CPAS to process mass spectrometry data generated from six types of mass spectrometry instruments on a centralized data processing pipeline for hundreds of proteomics researchers and users on the three campuses throughout the state of Indiana. This will give Indiana academic users a huge advantage in making sense of complex proteomics data for biomarker applications," said Dr. Chen.

CPAS and LabKey Server were developed through funding by the National Cancer Institute, the Fred Hutchinson Center, and the Canary Foundation, whose founder, Don Listwin, offered this statement on Canary's Web site: "[We] take a unique approach supporting research on early cancer detection. We know from experience in the commercial world that when all the key labs are using and building on the same software platform, they can focus their efforts on discovering biomarkers for cancer instead of reinventing the wheel."

For additional information visit http://informatics.iupui.edu/people/jakechen and http://informatics.iupui.edu.