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InforMax, Wellcome Trust Sanger Institute, EMC, Microsoft, IBM Research, Agilent Technologies, ISCB, MGED, GeneBio


InforMax Execs Promised Bonus Plan During Invitrogen Acquisition

Executives at InforMax are due to receive incentive bonuses if they stay with the company through the closing of its merger with Invitrogen, according to a Schedule 14D-9 filing with the SEC last week.

Under the plan, InforMax CEO Andrew Whiteley will receive an incentive bonus of $587,344, CFO John Green and CSO Stephen Lincoln will each receive $391,563, and Janet Lynch Lambert, vice president of marketing and business development, will receive $195,781.

According to the filing, the incentive bonuses are “based on a percentage of the valuation of InforMax in the change of control transaction.”

In addition, the merger provides that Invitrogen fund a $1.2 million pool for bonuses to InforMax employees who remain with the company following the merger.

Out of this pool, Whiteley will receive $87,182, Green will receive $73,814, and Lincoln will get a bonus of $58,121.

If Whitley is let go following the merger, he will receive an amount equal to his base salary and continuation of certain health benefits as severance. Whiteley’s initial salary was set at $375,000 when he joined the company in March.


SAN Storm: Sanger Taps Brocade for New Storage…

The Wellcome Trust Sanger Institute has moved from direct-attached storage to a networked storage model based on a SAN infrastructure from Brocade Communications Systems.

Sanger currently has 85 terabytes of data and expects it will add 60 to 80 terabytes of storage per year for the next five years.

Forty HP AlphaServer ES45 8-node server clusters will be networked with storage using the Brocade system. The storage network is being deployed by HP.


…While EMC Teams with Microsoft

EMC and Microsoft have partnered to develop the largest Microsoft SQL Server storage area network ever built, according to the companies.

The 45-terabyte configuration, developed for an undisclosed company, includes a simulated 10-terabyte human genomics database.

The project, which took place at Microsoft’s Redmond, Wash., SQL Server Labs, “will be used to showcase total-cost-of-ownership, management, and performance benefits of large-scale automated networked storage environments,” the companies said in a statement.

Gordon Mangione, vice president for SQL Server at Microsoft, said, “The 45-terabyte configuration demonstrates that SQL Server is highly scalable and can meet performance, management, and protection requirements. The end result is an integrated solution that allows customers to operate more efficiently and effectively.”


IBM Goes with Linux for Blue Gene Computers

IBM Research said it has chosen Linux as the main operating system for the Blue Gene family of supercomputers, which includes the petaflop-scale Blue Gene supercomputer for protein folding, as well as a smaller version called Blue Gene/L.

“We had two choices of operating systems for the BlueGene family, either use a special purpose system or Linux,” said Bill Pulleyblank, director of Exploratory Server Systems at IBM Research. “We chose Linux because it’s open and because we believed that it could be extended to run a computer the size of BlueGene. We saw considerable advantage in using an operating system supported by open source community so that we can get their input and feedback.”

Scaling Linux up to tera- and peta-scale supercomputers is expected to be a significant challenge. For this reason, IBM Research is currently running a large Linux cluster system to simulate Blue Gene, which will allow the Linux community to develop applications.

A small prototype of Blue Gene/L will be completed by the middle of next year.


Agilent to Offer Incyte’s Probe Data to Microarray Customers

Agilent Technologies has licensed probe sequence and annotation information from Incyte Genomics used in Agilent’s cDNA and oligo-based microarrays in order to make the data available to Agilent microarray customers.

Previously, this information was available only to customers of Incyte’s LifeSeq Gold, LifeSeq Foundation, and ZooSeq content databases.

Under the new agreement, Agilent microarray customers will have enhanced sequence annotation based upon the Proteome BioKnowledge Library Title Line, including the related protein structure, function, and disease-association information, hand-edited from the scientific literature, at no additional expense. In addition, customers will have password-protected access to microarray probe sequences for each gene probe.

The move mirrors a similar step Affymetrix took early this year, when it made its probe sequences available through its NetAffx website.


ISCB Seeks Award Nominations

The International Society for Computational Biology is seeking nominations from the bioinformatics community for several annual awards: the First Annual ISCB Accomplishment Award, which “recognizes senior members of the computational biology community who have made major contributions through research, education, and/or service,” and the Third Annual Overton Prize, which is awarded for outstanding achievement in the field of computational biology by a scientist in the early to mid phase of his or her career.

The Overton Prize was awarded to Christopher Burge of MIT in 2001, and David Baker of HHMI and the University of Washington this year.

Recipients of both awards will be invited to present keynote talks at next year’s Intelligent Systems for Molecular Biology conference in Brisbane, Australia, June 29-July 3, 2003.

Nominations for the 2003 prize should be sent to [email protected] before Friday, November 15, 2002.


MGED to Host Programming Jamboree

The Microarray Gene Expression Data (MGED) Society will hold its fourth MGED programming jamboree December 6-10 at the Carnegie Institution of Washington in Stanford, Calif.

The first day will be a tutorial session to educate the microarray community about the MAGE object model, the MIAME standard, and the relationship between them. The remainder of the time will be spent working on the MAGE Software Toolkit (MAGE-stk) to make it easier for people to use the model and generate MAGE-ML.

There is no charge for the meeting.


With UniProt on the Horizon, GeneBio Optimistic about Commercial Future

Formed as the commercial entity to handle industrial licensing arrangements for the cash-strapped Swiss-Prot database, Geneva-based GeneBio now nets between $5,000 and $100,000 per year per Swiss-Prot license from nearly every pharmaceutical company and biotech in the world.

But if the developers of UniProt — an NIH-funded project to merge Swiss-Prot with Trembl and the Protein Information Resource — get their way, GeneBio’s primary source of revenue will be made freely available to all users.

However, the company is confident it can remain afloat, even without revenue from UniProt. COO Nasri Nahas told BioInform’s sister publication ProteoMonitor last week that the company had already taken steps to “[go] beyond the database selling mode to other businesses in the field of biological knowledge,” citing its Melanie 2D gel analysis software and bioinformatics training courses as examples.

“Even if Swiss-Prot would…disappear from GeneBio’s licensing list, GeneBio, like any other company, had to rediscover itself, because since 1997, the market changed a lot, so we had to move with the market,” he said.

Nahas stressed that it’s still too early to know what the terms of access to UniProt will be once the current contract with Swiss-Prot expires at the end of 2004. There’s still a chance, he noted, that “the NIH would be willing, in three years, to follow the Swiss-Prot model. It’s a model that has proven to be efficient, where academic people have it for free, and the commercial people pay some price that will ensure the variability of the product and its quality.”

However, he added, “In the worst scenario case, we are prepared.”


Filed under

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.