NEW YORK, Nov. 19 – Academic researchers in countries that operate a mirror website to the GDB genome database have been unable to download fresh data since late last week, a source responsible for curating the main databank told GenomeWeb on Monday.
He added that in light of recent events with the GDB and a spate of sudden dismissals he was not able to determine whether the technical blackout was due to a technical glitch or deliberate action.
According to Connie Talbot, the GDB’s curator, a bioinformaticist in Australia on Friday informed him in an e-mail that researchers working from the GDB’s mirror site in Melbourne were unable “for a few days” to access new data to the main site.
GenomeWeb separately confirmed over the weekend with at least one researcher in Australia, Japan, China, and Taiwan that similar mirror sites in those countries would not allow access to updated data. Scientists in Japan, China, and Taiwan were unaware of any problem before being notified by a reporter, and Talbot explained that the nature of the problem would have meant that every country with a mirror site would have been locked out of fresh data.
There are currently several mirror, or ‘node’ sites listed on the main GDB site that feed into the GDB’s data hub at the Hospital for Sick Children, in Toronto. They are in Australia, Belgium, China, France, Germany, Israel, Italy, Japan, the Netherlands, Taiwan, and the US. These sites are also accessible directly through the main GDB website, www.gdb.org .
Talbot said he confirmed there was a problem with the node sites when he tried to check the ftp site and noticed that the DNS did not resolve its IP address. However, he stressed he did not know whether this was the result of a technical hiccup or a deliberate action.
However, he said that while a malfunction has not yet been ruled out, he believes that the lack of a recent precedent together with recent GDB-related events may indicate that foul play may have been involved.
“In the length of time that I’ve been dealing with this I have not seen this happen, that it was not fixed in a couple of days,” he said. “I would have thought that in this case that if they [the Hospital for Sick Children, which hosts the GDB] were working on it that I would have heard about it because I at least know about this stuff.”
Asked whether the service disruption was an uncommon occurrence, Talbot said that “it doesn’t go down. This is not something that we expect. We’ve been doing this since 1994 and since that time there have been problems. Things have gone down,” he said. “But these are extraordinary times” for the GDB and its leadership.
The HSC was not reachable for comment.
As GenomeWeb reported last week , A. Jamie Cuticchia, former principal investigator and director of the GDB, was abruptly fired on Nov. 2 and most of his personal and business files confiscated in a broad dispute between apparent efforts by him and the Hospital for Sick Children to commercialize the GDB and the ownership of the GDB domain name.
HSC spokeswoman Cyndy DeGiusti said that Cuticchia was "terminated with cause and the hospital has filed a notice of action, which is the preliminary step in a potential lawsuit asking for the return of a hospital asset."
The asset in question, DeGiusti said, is the www.gdb.org domain. "It appears from the information that our internal auditors have found that some of the staff in our bioinformatics center were working to commercialize an asset that the hospital owns without any involvement from the hospital."
At the heart of the dismissal, according to those close to the development, is the HSC’s assertion that Cuticchia overstepped his bounds by seeking to secure additional funding by organizing potential financial backers. According to the former directors, these backers would help commercialize the GDB for corporate use while keeping it free for academic researchers.
On the other hand, Cuticchia asserts that he was doing something that had already been approved by the HSC and that the hospital itself was seeking to commercialize the database.
DeGiusti denied that the HSC had at any time pursued commercialization of the GDB and argued that Cuticchia's efforts were not authorized by the hospital. However, files obtained by GenomeWeb show that the HSC in August 2000 had asked the research firm AngusReid to provide a potential market assessment. According to these documents, the HSC and Angus Reid had discussed between Aug. 1 and Aug. 14 ways in which the hospital may commercialize the GDB.
For their part, DeGiusti, Talbot, and others deny that the hospital has ownership to either the database or the domain name, and Cuticchia and an as-yet unconfirmed number of individuals were sued by the HSC on Nov. 5. It was not immediately known what the charges are in that suit, although an attorney representing him said that “the suit [is] frivolous in nature” and that “a variety of counter suits are anticipated.”
The HSC has also sued Talbot, who curates the data from Johns Hopkins University, in Baltimore, and Chris Porter, another director of GDB. According to the attorney who represents Talbot and Porter via GDB, the two men were charged on Nov. 1 with "misappropriation of the hospital’s resources, funds, proprietary interest, and business opportunities ... including the GDB domain name."
Talbot said that data are able to flow into the main GDB website but that they are not propagating through to the mirror sites. In any event, countries can access updated data directly from the main site, although the exercise in most cases would be very slow because of the nature of international Internet traffic.
“I‘m going to do my best to get this back up again,” Talbot said. “It is my hope that this is a technical problem that will be corrected.”
Sara Harris in Tokyo contributed to this report.