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GDB Staff Mulls Moving Main Database Node From Sick Kids to Oak Ridge National Lab


As researchers around the world reported difficulties downloading new data from GDB mirror sites last week, several supporters of the curated human genome database told BioInform that they were discussing available options for establishing a new core node for the site.

Although the technical difficulties that prevented researchers in Australia, Japan, China, and Germany from accessing updated records from GDB mirror sites for several days have been resolved, plans are in place to ensure uninterrupted access to the data by moving it to another site.

Steven Wallace, systems manager at the Bioinformatics Supercomputing Center at HSC, where the GDB is currently hosted, said the recent service disruptions were due to technical difficulties. “Glitches happen,” he said.

But these glitches — which were unprecedented in the history of the GDB according to head curator Connie Talbot — followed a bit too closely behind the controversial dismissal of GDB head Jamie Cuticchia and other GDB staff members for some supporters of the resource.

Last Tuesday, several GDB staff members met with the legal team at Johns Hopkins University, where curation of the database currently takes place, to discuss options for removing the main node from its current location at HSC to the Computational Biology group at Oak Ridge National Laboratory, which currently hosts the US mirror node.

“There’s a plan to move the node here,” said Ed Uberbacher, of the bioinformation systems group at ORNL. While the details of the move are still being worked out, Uberbacher said he believes “it can be done fairly quickly so there’s no interruption of service or curation.”

ORNL is currently assessing its software and hardware infrastructure to ensure it can support the database. “That involves Sybase and Oracle licenses and various amounts of RAID storage,” Uberbacher said.

Talbot confirmed that the meeting had taken place at Johns Hopkins but said it was too early to discuss any details of the proposed move. He said that Johns Hopkins “has been very supportive in seeing this resolved.”

While questions over IP rights to the database still remain, removing it from its current host shouldn’t be a problem, Uberbacher said. “There are numerous copies of the current data available, so it isn’t necessary to rely on the copy that exists at Sick Kids.”

It is expected that funding for the GDB at its new home will continue to come from the existing GDB budget — funding of over $50 million raised by Cuticchia while he was head of the resource at HSC.

And despite Cuticchia’s dismissal from his position at HSC, Uberbacher said, “As far as I’m concerned, Cuticchia remains the head of GDB and will remain so.”

— BT

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