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HapMap Project, Infocom, Inpharmatica, Open Access, Elsevier MDL, Alcon, Ocimum, Jubilant Biosys


HapMap Project Removes ‘Click-Wrap’ License Restrictions

The International HapMap Consortium last week said that it will remove the “click- wrap” license restrictions that have protected data generated by the project, and that all of the consortium’s data will now be completely open to the public.

The license was imposed to prevent outside groups from combining HapMap data with their own data to generate patentable inventions that could potentially be used to exclude other researchers from being able to freely use the HapMap data. The consortium therefore required users to sign a free, non-exclusive, non-royalty-bearing licensing agreement, by which they agreed not to prevent others from using the individual genotype data and to share data only with those who had also agreed to this condition.

“The licensing agreement was quite non-restrictive and enabled most researchers to use HapMap data as they wished. However, there was an unavoidable consequence of the license: It did prevent HapMap data from being incorporated into other public genomic databases,” said Francis Collins, NHGRI director, in a statement.

The consortium said that it decided to drop the licensing requirement for several reasons: The project has already publicly released data on about one million SNPs; Perlegen Sciences has publicly released genotype data on about 1.6 million SNPs; and new data-analysis methods have enabled the patterns of human genetic variation to be determined clearly enough from the primary genotype data to constitute prior art.

The decision will allow the HapMap project’s Data Coordination Center at Cold Spring Harbor Laboratory to distribute HapMap data to other public databases, such as NCBI’s dbSNP and the JSNP Database in Japan.

Infocom to Distribute Aureus Pharma’s Informatics Tools in Japan

Paris-based Aureus Pharma said last week that it has entered into an agreement with Infocom of Tokyo under which Infocom will distribute Aureus Pharma’s AurScope databases and software in Japan.

Infocom will market Aureas Pharma’s GPCR, ADME/Drug-Drug Interactions, and Ion Channel databases, as well as AurQuest, a web-based software product for interrogating the databases.

Inpharmatica Partners with Applied InSilico on ADME Software

Applied InSilico said that it has signed a contract with Inpharmatica to incorporate its ELE (Evolutionary Learning Environment) technology within Inpharmatica’s Admensa ADME platform.

Bioinformatics Seeks Comments on Open Access

The editors of the journal Bioinformatics, published by Oxford University Press, are conducting a survey to collect feedback on the issue of open access publishing.

“Your response has the potential to influence the future path of the journal,” the editors wrote in an open e-mail posted to several bioinformatics listservs last week.

Bioinformatics is currently published under a subscription-based model. “The major challenge faced by an established journal like Bioinformatics when considering open access publication is to find a viable model that will be attractive and accessible to authors and their institutions,” the editors wrote, “whilst allowing the journal to maintain its high quality, cover its costs (associated with submission, editorial review, production, dissemination, online functionality, archiving) and provide profit for investing in further development.”

The survey is available at:

Novartis to Use Inpharmatica’s Chematica Software

Inpharmatica said last week that the Novartis Institutes for BioMedical Research will use its Chematica technology to identify molecular targets under its bioactive compound project.

Financial terms of the agreement were not disclosed.

Chematica is the chemogenomics component of Inpharmatica’s PharmaCarta discovery informatics platform. The software aids target selection via druggability assessment and the identification of hits and leads against those targets.

Boehringer Ingelheim Licenses MDL’s Isentris

Elsevier MDL last week announced that Boehringer Ingelheim has licensed its newly released Isentris information management and integration platform.

Boehringer Ingelheim will use the platform in its worldwide R&D operations.

Financial terms of the agreement were not disclosed.

Alcon Awards University of Iowa $1.5M Bioinformatics Contract

The Center for Bioinformatics and Computational Biology, a joint enterprise of the University of Iowa College of Engineering and the Roy J. and Lucille A. Carver College of Medicine, said last week that it has signed a five-year, $1.5 million contract with Alcon Research of Ft. Worth, Texas, an ophthalmic pharmaceutical research company, for bioinformatics research aimed at preventing blindness.

The award, which will support research into the causes of age-related macular degeneration, extends an existing five-year, $1.5 million contract with Alcon that the center signed in 2003 to study glaucoma.

The UI researchers are developing bioinformatics software tools to identify potential therapeutic targets and to accelerate mutation screening of candidate genes for glaucoma and macular degeneration. According to UI, the software system will annotate and manage all gene-associated data, help identify and prioritize glaucoma and macular degeneration candidate genes, and identify potential therapeutic targets.

Ocimum Sells LIMS to Cerilliant

Ocimum Biosolutions said last week that it has sold its Pharmatracker LIMS platform to Cerilliant, a Texas-based chemical synthesis firm.

Cerilliant will use Pharmatracker to integrate and maintain multiple labs, Ocimum said.

Financial terms of the agreement were not provided.

Organon Licenses Databases from Jubilant Biosys

Jubilant Biosys said last week that it has sold a global license to its Kinase and GPCR ChemBiobase to NV Organon.

Financial terms of the licensing agreement were not disclosed.

Life Science IT to Benefit from $53M IU Grant

Indiana University said last week that a “centerpiece” of a $53 million Lilly Endowment grant awarded to IU Bloomington “will be the development at IU of new IT-based research in the life sciences through a major expansion and enhancement of the University’s information technology facilities and services.”

The Lilly grant was awarded to establish the Indiana Metabolomics and Cytomics (METACyt) Initiative, and was the largest grant IU Bloomington has ever received.

“A key goal of METACyt is to enable its scientists to perform massive new computer simulations and analyses not presently possible,” said Michael McRobbie, IU vice president for research and information technology.

The university said it is planning “a major expansion and enhancement” of its supercomputer, storage, and networking facilities to support the computational and data storage requirements of the initiative.

IU’s current computing facilities include a 2 teraflop IBM Linux cluster, a 1 teraflop IBM SP, a database complex of Sun systems, and a 2.4 petabyte data storage system.

Filed under

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.