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IBM, SimCyp, Pfizer, Compendia Bioscience, Biobase, InforSense, 454, ABI, Illumina, GeneGo, KineMed

IBM’s Roadrunner Surpasses Petaflop Barrier
Powerful enough to operate at a thousand-trillion calculations per second, or one petaflop, Roadrunner is the new IBM computer to be set up at Los Alamos National Laboratory. According to IBM, it would take the world’s six billion people each equipped with a handheld calculator more than 46 years to finish the computational tasks that Roadrunner can complete in one day.
The Department of Energy’s National Nuclear Security Administration this week announced the New Mexico development site for the $100 million project. Engineers at IBM’s Poughkeepsie, NY, plant built, tested, and benchmarked the supercomputer, which is named after New Mexico’s national bird. The machine will be transported on 21 tractor trailer trucks later this summer to Los Alamos.
Primarily intended for computational tasks associated with the US nuclear weapons arsenal, Roadrunner will also be used for genomics research, climate change studies, astronomy, and energy research. It runs on Linux and is energy-efficient, according to IBM, performing 376 million calculations per watt.
Roadrunner includes 6,948 dual-core AMD Opteron chips on IBM Model LS21 blade servers as well as 12,960 Cell engines on IBM Model QS22 blade servers. The system has 80 terabytes of memory, and is housed in 288 racks occupying 6,000 square feet.
Roadrunner is based on a so-called “tri-blade” configuration in which two QS22 blade servers and one LS21 blade server are combined into each tri-blade. The machine has a total of 3,456 tri-blades that were built in IBM’s Rochester, Minn., plant.
The Opteron chips handle standard processing tasks while CPU-intensive elements are directed to the Cell processors. Each tri-blade unit can run at 400 billion operations per second, or 400 gigaflops.
The system weighs 500,000 pounds, or around 223 tons, and its 10,000 connections — both Infiniband and gigabit Ethernet — require 57 miles of fiber optic cable.

Pfizer Study Finds SimCyp Accurately Predicts Drug-Drug Interactions
SimCyp said this week that scientists at Pfizer Global Research and Development recently published a study that validates SimCyp Simulator’s ability to predict the extent of drug-drug interactions for Pfizer's HIV drug maraviroc.
The results show that it is possible to predict clinically significant drug-drug interactions before undertaking human studies, according to the researchers, who published their results in the May issue of the British Journal of Clinical Pharmacology.
According to the paper, “the simulated median values were in good agreement with mean clinical changes,” such as increases in area under the plasma concentration time curve “although there was a trend for over prediction in the magnitude” of the drug-drug interaction by SimCyp.
Maraviroc, whose brand name is Selzentry, is a substrate for CYP3A4, an important enzyme in the body’s drug metabolism that is modulated by CYP3A4 inhibitors. For the study, the drug was metabolized to its N-dealkylated product and compared with three other CYP3A4-inhibiting HIV drugs: ritonavir, saquinavir, and atazanvir.
According to the study, “Simcyp has successfully simulated the extent of clinical interactions with CYP3A4 inhibitors, further validating this software as a good predictor of CYP-based drug-drug interactions.”

Invitrogen to Acquire Applied Biosystems for $6.7B
Invitrogen and Applied Biosystems said this week that Invitrogen will acquire all of the outstanding shares of ABI in a cash-and-stock deal valued at $6.7 billion.
The acquisition combines Invitrogen’s portfolio of reagents and low-cost instruments focused on the molecular and cell biology and protein research markets with ABI’s vast array of consumables and instruments for applications such as DNA sequencing, proteomics, RNAi, gene expression, and applied testing.
“There are some very compelling macrotrends that make this combination very attractive,” Invitrogen Chairman and CEO Greg Lucier, who will retain that position with the combined firm, said during a conference call this week. “It gives both of our companies access to high-growth markets, opening up opportunities for accelerated revenue growth.”
The deal follows a review conducted by Morgan Stanley that began last August, in which the bank was to give an opinion on a restructuring of ABI and its sister company Celera, both of which are traded as tracking stocks of parent firm Applera. That review led to a recent decision to split ABI and Celera, with the latter filing a registration statement to effect the change.
Applera Chairman and CEO Tony White said during the call that the split with Celera is proceeding, and ABI officials hope to get it done by the planned date of July 1. However, the split could be delayed depending on how quickly the SEC reviews and approves amended filings related to the split, said White, who will become a consultant to the combined company for five years.
He also noted that ABI had direct contact with other interested parties but narrowed its focus about five or six weeks ago to a merger with Invitrogen.
The deal would be the largest in the life sciences tools market since Thermo Electron bought Fisher Scientific for $10.6 billion in 2006. Similar to that deal, the combined operations of Invitrogen and ABI would create a nearly one-stop shop for life science research customers focused on end-to-end workflows.
The combined company, which will retain the Applied Biosystems name but will be based at Invitrogen’s headquarters in Carlsbad, Calif., will have approximately $3.5 billion in revenue, of which roughly 70 percent will come from consumables and services.
One area the firms are heavily focused on is the next-generation DNA sequencing market. ABI already sells the SOLiD system into this market, and Invitrogen has quietly been working on its own complementary technologies.
“Invitrogen is currently investing in third-generation sequencing technologies and would have been required to spend considerable resources to commercialize a system independently,” said Stevenson. “By combining our efforts in this area, the new company can accelerate these efforts and drive the cost of sequencing down toward the $1,000 genome, enabling new applications across research and applied markets.”
The merged entity will boast a sales and service force of approximately 3,000 employees and have customers in more than 100 countries. Lucier noted that the firm would spend more than $300 million annually on R&D, and employ over 1,000 scientists.
Following the first full year after close of the transaction, the firm expects to report mid-single digit organic revenue growth, and neutral to slightly accretive to earnings per share, said Invitrogen CFO David Hoffmeister, who will hold the same post with the combined company.
Under terms of the deal, ABI shareholders will receive $38 for each share they own in the form of Invitrogen stock and cash, with cash accounting for 45 percent of the split. The purchase price represents a 12 percent premium to ABI’s average closing price for the previous 30 trading days.
The firms expect the transaction to close in the fall, pending regulatory and shareholder approval.

Oncomine Identifies SPINK1 as Potential Biomarker for Prostate Cancer
Compendia Bioscience, a firm that provides cancer profiling data and analysis tools, said that its Oncomine software has helped to discover and identify SPINK1 as a potential therapeutic target and biomarker for prostate cancer.
Compendia CEO Daniel Rhodes, who is also a research investigator at the University of Michigan, led the Oncomine analysis that identified SPINK1 as a candidate oncogene in prostate cancer.
The results of the study were published in the current edition of Cancer Cell.
Compendia said that SPINK1-positive prostate cancers are a particularly aggressive subset of prostate cancer and that SPINK1 has a role in cancer invasion.
The company said that the analysis approach developed for the project is called Meta-COPA, and is slated to “soon” become a standard feature within the Oncomine platform.

Biobase Joins InforSense Open Workflow Partner Network
Biobase of Wolfenbüttel, Germany, said this week that it is partnering with InforSense in order to give joint customers of the two firms the ability to access Biobase’s software and databases within the context of the InforSense workflow analytics platform.
Through InforSense’s offerings, customers will gain access to Biobase’s Transfac, Transpath, and Proteome databases and its ExPlain application for analyzing high-throughput gene expression data.

GeneGo Licenses MetaCore to KineMed
GeneGo said this week that KineMed has licensed its MetaCore platform for use in an ongoing multi-center Phase II prognostic study of chronic lymphocytic leukemia.
GeneGo said that its genetic pathway database aligns with KineMed's phenotypic pathway analysis to facilitate identification of genetic polymorphisms and expression patterns that directly link genetics with KineMed's in vivo disease biomarkers.
KineMed's kinetic biomarker of CLL flux as a predictor of disease course is intended to stratify indolent versus aggressive disease.

RTI International Ceases to Host GDB
RTI International of Research Triangle Park, NC, has discontinued hosting the Human Genome Data Base, according to a statement from the National Center for Biotechnology Resources.
The reason for the closure is lack of interest in GDB data resources, NCBI said in a notice explaining that its Entrez Gene interface will no longer link to the resource. NCBI said that it plans to retain GDB identifiers in its records to support searching.
GDB was created in 1991 with funding from the US Department of Energy and the National Institutes of Health. It was originally hosted at the Johns Hopkins University School of Medicine and it later moved to the University of Toronto-affiliated Hospital for Sick Children.
RTI International began hosting GDB in November 2003.

Microsoft BioIT Alliance Adds Linguamatics 
Linguamatics, a company focused on text-mining, has joined the Microsoft BioIT Alliance, an association that aims to enhance collaboration and accelerate the pace of drug discovery and development.

454, ABI, Illumina Join 1000 Genomes Project
Illumina, Roche subsidiary 454 Life Sciences, and Applied Biosystems plan to boost the DNA sequencing power of the international 1000 Genomes Project, the National Human Genome Research Institute said this week.
The project is an international effort focused on expanding the Human Hap Map project by sequencing the genomes of 1,000 individuals, to provide a more comprehensive catalog of human genomic variation. 
The three companies each have agreed to sequence the equivalent of 75 billion DNA bases in the program’s pilot phase, generating the equivalent of 25 human genomes each over the coming year. They also have pledged to contribute additional sequence data over a three-year timeline.
Through a collaboration with the Human Genome Sequencing Center at Baylor College of Medicine, ABI has agreed to contribute an additional 200 billion bases of human sequence, according to NHGRI.
"The additional sequencing capacity and expertise provided by the three companies in the pilot phase will enable us to explore the human genome with even greater depth and speed than we had originally envisioned, and will help us to optimize the design of the full study to follow," said Richard Durbin of the Wellcome Trust Sanger Institute, who co-chairs the consortium.

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