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Feature - Medical Research on the Erasmus Computing Grid

Feature - Medical Research on the Erasmus Computing Grid

A simulated view of the three-dimensional architecture of genetic material as it appears in a human cell nucleus. Colors signify different chromosomes.
Image courtesy of Tobias A. Knoch, Erasmus Medical Center

Large portions of our DNA, it seems, serve no apparent purpose. Researchers in the field of genomics, however, are interested in all sections and levels of organization of an organism's DNA-from the DNA sequence to the overall morphology of a cell nucleus.

Scientists in the Biophysical Genomics Group in the Department of Cell Biology and Genetics at Erasmus Medical Center in The Netherlands believe that the genome has much to tell us. A consortium of researchers, using the new Erasmus Computing Grid, seek to determine the three-dimensional structure of the human genome. They hope that looking at the shape of all our genetic material as a whole will give us a more complete understanding of how our bodies maintain and reproduce themselves.

"We would like to understand the genome completely and how it functions as a single unit-as an entire system," says Tobias A. Knoch genomics researcher and head of the Erasmus Computing Grid. "Each level of organization is important-it's not just the DNA sequence."

Their findings so far are exciting. Our chromosomes do not wind up in a random fashion, but in an organized, albeit extremely complex way. Researchers count about seven separate levels of structured organization. Chromosomes loop and fold in a way that lets the areas of DNA which are most often used to be accessed easily. Also, because of the genome's architecture, most molecules and proteins can reach the areas where they are needed by simple diffusion-without extra energy input from the cell.

The modeling work of this team and many others at Erasmus Medical Center, the largest hospital and biomedical research center in The Netherlands, is computationally intense. The Erasmus Computing Grid infrastructure, still in its growing phase, comprises the desktop computers of the Medical Center and of an affiliated school, the Hogeschool Rotterdam, and serves the staff in clinical practice, medical research and teaching.

"With 15 user groups, we use the grid for many research areas," says Knoch.

The grid currently runs at a power of about 7,000 CPUs, with more desktop computers from the contributing institutions to be incorporated soon. This will bring the total power to about 30,000 CPUs.

The Erasmus Medical Center and the Hogeschool Rotterdam use the ECG in a host of research areas: image analysis, mass spectroscopy, gene sequencing, osteoporosis research with computer tomograms, protein structure prediction and microscope image analysis, to name just a few.

To learn more about the research at Erasmus Medical Center visit their Web site.

-Danielle Venton, iSGTW Editor

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