New Web Service Will Speed Up Bioinformatics Research
The Ohio Supercomputer Center (OSC) and University of Cincinnati’s Genome Research Institute (GRI) are recruiting research biologists at the Ohio Collaborative Conference on Bioinformatics (OCCBIO) this week and at other venues to help test its new computational biology tool as an initial project of the Ralph Regula School of Computational Science.
As an initial project of the Ralph Regula School of Computational Science, the Genome Research Institute Discovery Platform, or GRIDP, is a joint effort between OSC and GRI for bioinformatics researchers who do not have advanced computer programming training. The new tool is a web service that lets scientists replace the command code writing process necessary for using high performance computing (HPC) and computational biology software with a simpler point-and-click XML interface.
Dr. Steven Gordon, Ralph Regula School of Computational Science interim director and OSC director of resources and planning, said the GRIDP project’s primary goal is to use the Third Frontier Network (TFN) to provide better access to shared computational tools, such as traditional bioinformatics packages BLAST and Primer3, for education and research.
The Ralph Regula School of Computational Science, established by the Ohio Board of Regents, OSC, and the Ohio Learning Network (OLN) will be used to disseminate information about GRIDP’s production version so that other universities will have access to this new system. The Ralph Regula School is a virtual institution that builds on the tremendous assets Ohio already possesses, including the TFN and OSC’s Blue Collar Computing initiative, to expand computational science capabilities to colleges and universities, as well as small- and medium-sized companies in Ohio.
Dr. Matt Wortman, GRI director of computational biology and information technology, said he wants to recruit 15 to 20 beta testers to help with the final GRIDP development. He said beta testers will have exclusive access to OSC’s powerful cluster, as well as new software that manages databases and moves data between processors.
Wortman said the project started to help alleviate the technical challenges of writing command codes necessary for researchers to use HPC, particularly in his field of drug discovery, in which codes can be hundreds of characters long and require programming knowledge that exceeds the capabilities of the average scientist. He said performing calculations on the wrong files due to similar file names or naming mistakes are also obstacles to using HPC for biological research.
“This was a deal breaker for most non-computational folks because the time it takes to get up to speed on code writing eclipses any near-term benefit,” Wortman said. “The new service will allow bioinformatics researchers to spend more time conducting research and less time writing the command codes required for using high performance computing.”
Dr. Thomas Freeland, Walsh University associate professor of biology and director of bioinformatics, indicated that his institution’s faculty and students are eager to use the new GRIDP platform for genetics, biochemistry, microbiology, cell biology and more to help improve teaching and learning.
“GRIDP will allow us to make use of more sophisticated bioinformatics functions that we don’t have the computer expertise to use at the moment,” Freeland said. “The people who think of interesting questions often don’t know what type of computing can be utilized to answer those questions, and the people who understand the computing have a hard time grasping the questions.”
“We need to make sure graduates in biology understand that computational science is going to be a big part of their future, and we need to give them access to it right away,” Freeland added. “GRIDP is a step in that direction.”
GRIDP also uses a cluster computer at OSC-Springfield to run its software. OSC has technical staff working on program implementation and coding so that GRIDP will run on its production machines after the initial test period.
The Ohio Board of Regents is sponsoring this Ralph Regula School project with $600,000 in funding made available by Congressman Ralph Regula, (R-Navarre) through the U.S. Health Resources and Services Administration Office for the Advancement of Telehealth. The project started in May 2005 and will run through the summer of 2007.
Persons interested in the GRIDP beta testing project may contact Matt Wortman at matt.wortman@uc.edu or 513/558-4915.
About the Genome Research Institute
The Cincinnati Genome Research Institute, www.gri.uc.edu, is a state and regional hub for gene and protein profile analysis, bioinformatic software development, and medicinal chemistry. Funded in part by a $9 million grant from Ohio's Biomedical Research and Technology Transfer (BRTT) Commission, the GRI facilitates collaborative projects between the University of Cincinnati, Cincinnati Children's Research Foundation and various commercial partners. More information is available at http://gri.uc.edu/.
About OSC
OSC serves Ohio by connecting HPC, the nation’s foremost state-of-the-art research network, and a deep pool of expertise dedicated to advancing research in the public and private sectors. OSC plays a key role in fueling Ohio’s emerging high tech economy by enabling frontline research, cutting-edge information technology, and new industrial growth. More information is available at http://www.osc.edu.
About the Ohio Board of Regents
The Ohio Board of Regents is the coordinating body for higher education in the state. Established in 1963 by the General Assembly, the 11-member public board has a direct, non-governing relationship with all of Ohio’s colleges and universities. More information is available at http://www.regents.state.oh.us.
