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Bioinformatics Briefs: Dec 17, 2001



The European Union has made its report, “Workshop Report on Managing IPR in a Knowledge-Based Economy — Bioinformatics and the Influence of Public Policy,” available via ftp at life/ docs/ipr_bioinf.pdf.

The report is based upon a workshop held in Brussels, Belgium, on September 11-12, where participants identified a number of challenges facing bioinformatics in Europe. Many emerging problems, according to the report, involve links between intellectual property rights (IPR) and public policy.

Specific problem areas identified include underfunding in the EU; lack of awareness among academics that IPR can be used strategically for knowledge management at all stages of research and innovation; economic vulnerability of European bioinformatics companies; escalation of costs due to royalty and license fee stacking; fragmented national and EU funding policies; and a lack of coherent policies to deal with the rapid growth rate of primary data.

The report proposes several guidelines to address these challenges, including appropriate use of IPR protection to achieve strategic institutional objectives; strategic university management of database IPR; international collaboration agreements allowing for diverse IPR systems; and database publishing guidelines.

“All involved sectors strongly support a comprehensive and up-to-date publicly available and free set of bioinformatics data, while recognizing the need of large pharma companies to access a mixture of high-quality public and private databases and tools,” noted the report.

Last week, the Board of Directors of the International Society for Computational Biology issued a position statement in support of the Public Library of Science, an initiative to make all scientific literature freely available in the public domain.

The resolution stated, “The ISCB supports the proposal of the Public Library of Science (PLoS) initiative to allow free public access to all scientific journal publications after a limited time during which the publisher may hold copyright control. Therefore future contracts with publishers regarding journals and conference proceedings affiliated with the ISCB will require that the publisher agree to release the published material into the public domain, in substantial agreement with the PLoS policy.”

Additional information on the PLoS is available at




At a three-hour meeting for investors held in New York last week, Jason Molle, general manager of Celera Genomics’ online business, spoke of the company’s plans to develop its data business into the “gold standard” for data. “No company has solved the problem of effectively managing or integrating” all of the genomic data currently available, he said. “We want to be the one-stop shop for users.”

Craig Venter, the firm’s president, meanwhile, promised that revenue for Celera’s online data business would surge 40 percent to 50 percent and “will be profitable this year.” Molle supported this by predicting $250 million growth in annual revenue and an increase in subscribers to 50,000 over the next two years.


New York-based Cognia was awarded a Phase I Small Business Innovation Research grant from the National Science Foundation to create a comprehensive database resource on protein localization.

The protein localization database will address all eukaryotic systems with an emphasis on human proteins and their orthologs, the company said.

“The NSF award will support an innovative database system to provide context to proteomics data,” said Cognia CEO David Rubin in a statement. “This system will be especially powerful when combined with our synergistic protein catabolism database system.” The company expects the database to accelerate the development of drugs that manipulate protein location in order to modulate function and inhibit disease pathways.




EraGen Biosciences of Madison, Wis., has entered a research agreement with McGill University to develop algorithms for the design of universal DNA microarrays that are not specific to a single organism or set of genes and will allow for simultaneous monitoring of multiple hybridizations.

McGill will work closely with EraGen to develop the algorithms for the array designs. The first phase of the project will build on existing algorithms to use EraGen’s proprietary AEGIS bases in universal hybridization sequences. The second phase will develop software that uses a thermodynamic model to detect DNA secondary structure formation.

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