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News Briefs from the TIGR Genome Sequencing & Analysis Conference

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Venter May Go for Green Computing at TIGR/TCAG Facility

Craig Venter said his new foundation is busy and growing rapidly, with plans to hire a total of 79 people to run a planned sequencing facility for TIGR and the TIGR Center for the Advancement of Genomics.

In an interview with BioInform and its sister publication GenomeWeb.com during the GSAC meeting, Venter said the decision on whether to go with ABI or Amersham sequencers for the new facility is “getting down to the wire.”

As for the computational requirements for the center, “we’re talking to the top computer manufacturers,” he said, adding, “it’s sort of like déjà vu all over again.”

There will be differences, however. “The 1.5 teraflop computer we built at Celera was built to assemble the human genome. … It’s not an economical way to build the kind of compute facility we need going forward. We were in a big hurry.”

The new goal will be “to build something that is replicable so any major medical center in the US or around the world can have a chance to do the same level of computing.”

Marshall Peterson, who helped build the computer at Celera but left the company before Venter did, is heading up the buying decision. The group is considering energy-efficient computers such as the “Green Destiny” supercomputer at Los Alamos National Lab, which is based on RLX blade servers and Transmeta processors. “We’re trying to come up with almost the opposite of what we did at Celera,” he said. “Simple, cheap, replicable supercomputing.”

A big part of that cost reduction will have to come from a reduction in air conditioning, he noted. “The room at Celera cost $6 million before you put the computer in. That makes it pretty expensive. If for any hospital to interpret the genetic code of their patients they need a $100 million computer, this is not a revolution that will go very far.”

 

Gene-IT Refocuses, Adopts Single-Product Strategy

Gene-IT, a bioinformatics software firm based in Paris, France, and Worcester, Mass., said it is refining its product strategy in line with a renewed focus on comparative genomics.

The company has merged its LASSAP sequence comparison software with its Biofacet genome clustering software to create a single product that will be sold under the Biofacet name. Biofacet processes the company’s Sequence Mining Language (SML), a set of command modules for genome database management, genome-scale sequence comparison, and genome clustering. Ron Renauro, vice president of worldwide business development at Gene-IT, said the company wants Biofacet to be considered “the language of comparative genomics.”

In addition, the company has moved to a perpetual licensing model. Subscription-based models are not in line with customer wishes to “make the software part of their production workflow,” Renauro said.

 

Journals Endorse MGED Data Standards

The Nature journals and The Lancet have publicly endorsed data standards for microarray experiments proposed by the Microarray Gene Expression Data (MGED) society, according to Alvis Brazma, head of the microarray informatics group at the EBI.

Brazma noted during a talk at the GSAC meeting that the journals will make the Minimum Information About a Microarray Experiment (MIAME) guidelines a standard requirement for authors submitting microarray data for publication.

Additionally, the Nature journals will require submission of microarray data to a public database.

Brazma said the journal Cell has expressed an interest in following the standards as well.

The journals responded to a recent open letter from MGED, which strongly urged them to use a set of guidelines and a checklist based on the MIAME standard in their decisions to accept microarray papers for publication. Their reply was quick: “We sent this open letter to the journals just a few weeks ago, and The Lancet called me back the next day,” Brazma told BioInform’s sister publication, BioArray News.

 

GeneData Celebrates a Birthday

GeneData, headquartered in Basel, Switzerland, celebrated the one-year anniversary of its US base of operations in Cambridge, Mass., during the GSAC meeting. Those employees not manning the company’s booth in the Hynes Convention Center were treated to a celebratory luncheon party courtesy of Andrew DePristo, president of the US subsidiary.

The company is sticking to the very focused market it has defined for itself, DePristo told BioInform: Enterprise-scale software systems for microarray analysis, and research collaborations that leverage the company’s expertise in anti-infectives research.

The down market has not tempted the company to deviate from what it sees as its core competencies, DePristo noted. “Companies approach us that have a few people doing 20 chips a year and we tell them to go with another solution,” he said.

“The market’s not great,” DePristo summed up, “but it’s not terrible.”

 

HP Claims Number-One Spot in Life Sciences

Despite the loss of one of its premier life science customers just prior to the GSAC meeting, Hewlett Packard’s booth literature trumpeted the fact that the company still holds the largest market share in life sciences information technology.

The top spot is largely due to the merger between Compaq and Hewlett-Packard, which broadened the customer base — and definition — of what each company considered to be the life sciences market prior to their merger. “Compaq was very strong in discovery, while HP was strong in clinical trials and other areas of pharma,” said Lionel Binns, worldwide life and materials science manager. The result, he said, is “a broadening view of life sciences” for the combined company.

If Binns harbored any hard feelings over the loss of its Celera account to IBM [BioInform 09-30-02], it was barely detectable. Crowing over the $22 million deal the company recently signed with the Sanger Institute, Binns was quick to note that IBM would not disclose the financial details of its agreement with Celera.

While acknowledging that IBM is far and away HP’s biggest competition for the top spot in the life sciences market, Binns said he’s confident about the company’s future. The merger has “had a positive effect on our current clients” he said, because there’s security in having a larger supplier. “Questions around the merger are behind us and a lot of the earlier doubts have gone away,” he noted.

Some business was lost due to the merger process, but “the path forward looks pretty clear,” he said.

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