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Blueprint, SRI, IBM, European Union Software Patent Ruling

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Blueprint Secures Funding for BIND, Releases Curation Standards

The Blueprint Initiative housed at Mount Sinai Hospital’s Samuel Lunenfeld Research Institute has secured Can$29 million (US$21.3 million) from Genome Canada, the Ontario Government’s Research and Development Challenge Fund, and the Canadian Institutes of Health Research, to support continued development of the Biomolecular Interaction Network Database.

Separately, Blueprint announced that it has released a curation reference document and a curation training manual through its website (http://www.bind.ca/index. phtml?page=manuals) “in order to show funding agencies and journals around the world that by January, 2004, they will be fully prepared for major funding agencies and journals to make BIND submissions a required condition of publication.”

The funding from the Canadian government, originally promised in May 2001, was delayed when the initiative’s original industrial partner, IBM, pulled out of the effort earlier this year [BioInform 02-10-03]. With Sun Microsystems as its new industrial partner, along with $5 million worth of computer equipment, the effort’s public funding is now secure under Genome Canada’s matching grant program.

The Blueprint initiative will use the additional funding to enter a backlog of 80,000 molecular interaction records into the database. Blueprint’s current staff of 59 is expected to grow to 77 by 2005.

 

SRI Creates Consortium to Curate Human Pathway Database

The BioCyc collection of pathway/genome databases has moved well beyond the world of E. coli and other microbial organisms. With last month’s release of BioCyc 7.1, SRI International added HumanCyc to its more familiar EcoCyc and MetaCyc options. HumanCyc, which contains information on 28,783 genes and 134 predicted human metabolic pathways, was built using SRI’s PathoLogic software and a minimally redundant human gene set from Ensembl, LocusLink, and GenBank.

Now, according to Peter Karp, director of the bioinformatics research group at SRI, the challenge will be in manually curating the database by adding new data from the scientific literature. SRI is creating a consortium of private companies to support the manual effort, Karp told BioInform. “We’re soliciting companies to join up and contribute funds for curation,” he said.

Several companies have already agreed to provide funding for the project, Karp said. While the database itself is freely available to anyone via the BioCyc website, members of the consortium will get access to a downloadable version of the data six months before it becomes available online.

 

IBM Links with SAS, Launches New Academic Support Program

IBM’s life sciences group last week entered a co-marketing agreement with SAS and kicked off a new initiative to support life science research at academic institutions.

In the three-year agreement with SAS, the companies agreed to jointly market SAS’s analytic solutions with IBM hardware, software, middleware, and services. The agreement builds on a strategic alliance the companies first entered in August 2001 for the financial services and telecommunications industries.

On the academic front, IBM launched its Institutes of Innovation program, which provides non-profit research institutions with early access to IBM technologies, software, and technical support; post-doctoral and research associate opportunities; assistance with external funding applications; and the opportunity to take part in IBM’s university award programs.

Indiana University and Johns Hopkins University have been selected as the first two participants in the program.

IBM already awards SUR (shared university research) grants to academic institutions engaged in life science research. An IBM spokeswoman said the new initiative is “more extensive” than the SUR program because it offers funded assistantships and technical support, and is a multi-year collaborative program as opposed to the one-time, one-year SUR awards.

 

EU One Step Closer to ‘Technical’ Software Patent Ruling

The European Union’s legal affairs committee on June 18 voted to adopt a proposed ruling on the patentability of computer-implemented inventions by 20 votes to 8 with 1 abstention.

Unlike the current software patenting policy in the US, which permits a broad range of computer-related patents, the EU directive requires that a patentable computerized invention have an industrial application and involve a technologically inventive step.

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The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.