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Stratagene to Develop Free ‘Lite’ Software for Affy Customers

Affymetrix and Stratagene last week announced a non-exclusive partnership under which Stratagene will develop a new software package for microarray analysis called ArrayAssist Lite.

The software — a limited version of Stratagene’s ArrayAssist package — will be freely available to Affymetrix’s existing GeneChip customers via the Internet in April. Affymetrix said it will also begin pre-installing the software on new GeneChip workstation desktops at that time.

The companies said that ArrayAssist Lite will support a number of Affymetrix-format data files and reports, including RMA, GC-RMA, MAS5, and PLIER, a new signal estimator.

Affy customers will have the option to upgrade to the premium version of ArrayAssist, which provides more advanced analytical capabilities, such as gene clustering, pattern detection, and interactive visualizations.


Accelrys Sublets Former Headquarters, Reduces Quarterly Loss

In an 8-K filing with the US Securities Exchange Commission last week, Accelrys disclosed that it is subleasing its former headquarters in San Diego, Calif.

Under the terms of the sublease agreement, Accelrys will receive monthly rental payments that will “offset the loss on abandonment of the facility recorded during the quarter ended December 31, 2004,” the company said in the filing. This loss was reported as $4.7 million in the company’s quarterly earnings report [BioInform 01-31-05].

Accelrys said in the 8-K that the payments will reduce the loss on abandonment by $1.1 million, to $3.6 million, and will reduce the reported net loss per share for the quarter to $.18 from $.22.


ABI, Celera Revise CDS Royalty Agreement

Applied Biosystems and Celera Genomics have revised the terms of a 10-year royalty agreement for the Celera Discovery System that the companies initiated in 2002 [BioInform 04-29-02], according to Applied Biosystems’ most recent 10-Q filed with the US Securities and Exchange Commission.

Under the original agreement, ABI became the exclusive distributor of CDS and other products and agreed to pay a royalty through the end of fiscal 2012. The original royalty rate was progressive with the level of sales through fiscal 2008, up to a maximum of 5 percent. Beginning in fiscal 2009, the rate was to become a fixed percentage of sales, declining each succeeding fiscal year through fiscal 2012. For fiscal 2005, the royalty rate is expected to be 3 percent.

Under the revised agreement, the royalty rate will be fixed at 4 percent, beginning in fiscal year 2006 and running through the length of the agreement, which has been extended to 2017.

In addition, Applied Biosystems has agreed to reimburse Celera for any “shortfall” in earnings during the 2003-2006 fiscal years below $62.5 million, “if the shortfall is due to the actions of the Applied Biosystems group including changes in marketing strategy for CDS.”

Current products besides CDS that generate royalties under the agreement include ABI’s TaqMan assays, SNPlex genotyping system, VariantSEQr resequencing system, arrays used with the Expression Array System, and TaqMan low-density arrays.

In its 10-Q, ABI said that its “experience with the development and commercialization of products covered by the agreement has varied from the original assumptions on which the terms and conditions of the agreement were established.”


Two NIH Bioinformatics Methods Available for Licensing

The National Institutes of Health is out-licensing two bioinformatics analysis methods developed by scientists at the National Human Genome Research Institute.

The methods, one entitled, “Methods for Analyzing High Dimensional Data for Classifying, Diagnosing, Prognosticating, and/or Predicting Diseases and Other Biological States,” and the other entitled, “Selections of Genes,” were both developed by Javed Khan, Paul Meltzer, and NHGRI colleagues.

The first method is a general approach to using supervised artificial neural networks to classify, diagnose, predict, or prognosticate various diseases. The second specifically uses ANNs to classify cancers using gene expression data.

Licensing terms were not provided, but an NIH spokesperson said that all the institute’s licensing arrangements are negotiable.

Interested parties can contact Cristina Thalhammer-Reyero at [email protected].


Compugen’s Q4 Revenues Sink 60 Percent

Compugen last week reported a 60-percent decline in fourth-quarter revenues and a 20-percent jump in net losses.

Revenues for the three months ended Dec. 31, 2004, sank to $552,000 from $1.4 million in revenues for the same period in 2003. $393,000 — or 71 percent — of the company’s income was in the form of government grants.

Compugen attributed its slide for both the fourth quarter and fiscal year 2004 to the discontinuation of its “non-strategic” bioinformatics products and services and its new focus on diagnostics and drug discovery.

R&D spending in the quarter increases slightly to $3.5 million from $3.3 million year over year.

Fourth-quarter net losses widened to $3.7 million from $3.5 million in the year-ago period.

As of Dec. 31, Compugen had $20.6 million in cash, cash equivalents, and short-term marketable securities.


NCI Seeks Small Businesses to Build Informatics Infrastructure

The National Cancer Institute last week issued a request for comment/source sought notice entitled, “Development of a Common Biospecimen Coordination System and Informatics Infrastructure for NCI Prostate Specialized Programs of Research Excellence (SPOREs).”

NCI said it is seeking two or more qualified small business contractors capable of implementing a biospecimen coordination system and informatics infrastructure for multiple NCI SPOREs in prostate cancer research.

The system should enable distributed researchers to share biospecimens and data, NCI said. The project will serve as a pilot for a proposed National Biospecimen Network. If the pilot project is successful, “the government intends to use the Biospecimen Coordination System developed by the contractor for other NCI and government projects,” NCI said in the notice.

The complete text of the notice, number SS-NCI-ESS-2005, is available through NCI’s Research Contracts Branch website (http://rcb.nci.nih.gov/).

Capabilities statements are due Feb. 18.


Jubilant, Genomics Collaborative in Integration Deal

Jubilant Biosys said last week that users of its PathArt database will now be able to link directly to information in Genomics Collaborative’s Global Repository — a biorepository of tissue, serum, DNA, and RNA from 120,000 donors.

Jubilant said that the integration will enable researchers to immediately determine the availability of tissue from disease states and physical sites that involve pathways of interest.


VBI to Provide Microarray Analysis for Army

The US Army Medical Research Acquisition Activity, the contracting element of the US Army Medical Research and Materiel Command, has issued a presolicitation notice stating that it proposes to award a contract to the Virginia Bioinformatics Institute for microarray analysis services.

The notice states that VBI was awarded the contract “on a sole-source basis … in order to guarantee the best correlation between previously generated microarray data in our laboratory and the new ones to be generated to reduce technical variability.”

Financial details and other terms of the contract were not provided.

 

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In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.