Using a gift of hardware and software from IBM, researchers at Johns Hopkins hope to speed up their efforts to create computer models that reveal how genes and proteins inside human cells can influence the development of heart disease. By studying the origins of heart disease at the cellular level, the researchers hope to produce a computer tool that can help develop drugs to halt or reverse these illnesses.
Such research requires sophisticated software and hardware with the ability to store and manage massive amounts of data. To advance this effort, IBM recently provided additional computing equipment to Johns Hopkins under its Shared University Research awards program.
The grant is being used by two teams of researchers. One group is assembling highly detailed computational models of the heart and other organs. The other is devising software that allows large amounts of data to be shared easily and efficiently by researchers working in separate locations.
"I'm ecstatic about this," said Raimond Winslow, director of the university's new Center for Cardiovascular Bioinformatics and Modeling, which involves researchers from the Whiting School of Engineering, the School of Medicine, Queen's University in Ontario and the University of California, San Diego. "This equipment will really accelerate the work we're doing here."
In their efforts to find out what triggers heart disease, Winslow and his colleagues are measuring and recording the behavior of thousands of genes at one time. "In many diseases, there are significant changes in gene expression," said Winslow, a professor in the Department of Biomedical Engineering. "That's what we need to characterize--which genes are switched on or off and which sequences have important health consequences. Our job is to identify disease mechanics at the gene and protein levels, then identify a drug target that might be useful in treating the disease."
To accomplish this, Winslow's team is amassing an enormous amount of numerical information. To manipulate and store this data, the researchers used their portion of the IBM grant to acquire an IBM P690 computer equipped with 16 microprocessors and 64 gigabytes of memory, a fibre-channel storage area to house data in a central site that can be accessed by many computers, a robotic tape system that can store 28 terabytes of data and a large suite of software products to assist in managing large databases.
The other key Johns Hopkins recipient of the IBM grant is Randal Burns, assistant professor in the Department of Computer Science and director of the Hopkins Storage Systems Lab. Burns is a former IBM researcher who served as chief architect for a software product called Storage Tank, which is expected to be available later this year. At Johns Hopkins, Burns has used a portion of the IBM grant to acquire a 7-node xSeries Linux-based computing cluster. Burns will use the hardware in an effort to develop new global-scale file management software that will allow researchers and businesses in different locations to access and manipulate information stored at many sites. "Large-scale file systems are exciting in that they support collaborations like the Center for Cardiovascular Bioinformatics and Modeling by allowing researchers to share information among campuses across the globe," Burns said.
Under the terms of the grant, Johns Hopkins researchers will collaborate with IBM computer scientists regarding findings that may have applications in other laboratories or businesses, particularly in connection with advances in the life sciences.
"Johns Hopkins University is clearly a leader in biomedical research," said Beth Smith, director of IBM Life Sciences Solutions Development. "The creation of the new Center for Cardiovascular Bioinformatics and Modeling will be a strong catalyst for cross-disciplinary collaboration and will advance the use of information technology in discovery research. IBM is delighted to be Johns Hopkins' technology partner."
IBM's Shared University Research program awards computing equipment (servers, storage systems, personal computing products, etc.) to institutions of higher education around the world to facilitate research projects in areas of mutual interest, including life sciences, grid computing, autonomic computing and deep computing.
These SUR awards also support the advancement of university projects by connecting top researchers in academia with IBM Research personnel, along with representatives from product development and solution provider communities. IBM awards approximately 50 SUR grants per year worldwide.