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Genetic Privacy, BioAnalytics Group, BioSoftware Systems, Genomatica, Jubilant Biosys, Strand Genomics, Compugen, Gene-IT, Fujitsu, ViaLactia, Visualize, Insightful

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Stanford Researchers Question Adequacy of Genetic Privacy Protection

In a Policy Forum article in the July 9 issue of Science, Russ Altman and colleagues at Stanford University argued that unencumbered access to genomic data raises unforeseen privacy issues, and that current attempts to protect genetic data are inadequate.

“Nobody did a careful calculation to find whether ‘anonymous’ patients could be identified from this [genomic] data,” said Zhen Lin, a scientist in Altman’s lab who led the study, in a statement.

While the Health Insurance Portability and Accountability Act (HIPAA) of 1996 requires that research data be stripped of identifying information such as names, addresses, and other demographic information, the law does not address use or disclosure policies for human genetic data, the authors wrote.

“Traditionally people believe that if there is no identifier attached, then the sample is anonymous,” Lin said. “We found that’s really not true because the DNA code itself is an identifier.” In their paper, the researchers argue that surprisingly small amounts of genomic sequence data are enough to identify an individual to a high degree of accuracy. “Specifying DNA sequence at only 30 to 80 statistically independent SNP positions will uniquely define a single person,” they wrote. “Furthermore, if some of those positions have SNPs that are relatively rare, the number that needs to be tested is much smaller.”

Without adequate protection for genetic data, the authors argue, a person could match genetic information about a former research subject to publicly available databases to get personal medical information about the subject.

Altman and colleagues recommended “explicit clarifications to rules and legislation (such as HIPAA), so that they explicitly protect genetic privacy and set strong penalties for violations.”


BioAnalytics Group, BioSoftware Systems Ink Joint Deal with Roche

The BioAnalytics Group and BioSoftware Systems said last week that they have entered into a joint partnership to provide Roche with physiological models to support the company’s drug discovery efforts.

Scientists at the BioAnalytics Group and Roche will use BioSoftware Systems’ BioPathway Explorer modeling software to develop simulation models of biological systems.

Financial terms of the deal were not provided.


Genomatica Licenses SimPheny to Wageningen

Genomatica said last week that it has licensed its SimPheny modeling platform to the Wageningen Center for Food Sciences in the Netherlands for use in the center’s microbial research program.

The licensing agreement is part of a collaborative project under which Genomatica and the Wageningen Center will co-develop an in silico metabolic model of Lactobacillus plantarum — a lactic acid bacterium used to improve the flavor and texture of food and to extend the shelf-life of food products.

Financial terms of the agreement were not provided.


NCI Licenses Two Jubilant Biosys Databases

Jubilant Biosys said last week that the National Cancer Institute has licensed two of its biological databases.

NCI licensed the company’s Kinase ChemBioBase database of small molecules and kinase targets, along with its PathArt database of manually curated pathways.

Financial terms of the agreement were not provided.


CombiMatrix to Co-Market Strand Genomics’ Microarray Analysis Software

Acacia Research’s CombiMatrix microarray business will market Strand Genomics’ gene expression analysis software, the companies said last week.

Under the agreement, Newport Beach, Calif.-based CombiMatrix will co-market Strand’s Avadis software.

The companies will also co-develop an interface for ordering CombiMatrix CustomArray products through Avadis.


Compugen Launches Small-Molecule Spin-off

Compugen last week announced that it had formed a new subsidiary, Keddem Bioscience, that will be focused on small-molecule drug discovery.

Compugen will transfer its internal chemistry division to the new firm, which will be located in Ashkelon, Israel.

Keddem will use in silico methods to design small-molecule modulators for protein targets based on the “proposed creation of a comprehensive, yet relatively small set of carefully designed molecules and a suite of algorithms.”

The set will contain fewer than 100,000 molecules, Compugen said. When synthesized, Keddem will screen the molecules and analyze the results with a suite of proprietary algorithms designed to provide three-dimensional information about the active site of the target.


NSF Earmarks $8M for Integrative Biological Research Projects

The US National Science Foundation has launched an $8 million program called Frontiers in Integrative Biological Research to support research that involves “integrating the scientific concepts and research tools from across disciplines including biology, math and the physical sciences, engineering, social sciences, and the information sciences,” according to the program announcement.

US academic institutions and non-profit research organizations as well as consortia of these organizations are eligible. Research looking at specific diseases is not supported under the program.

NSF plans to award up to eight projects under the program in the 2005 fiscal year. Preliminary proposals are due Oct. 4.

Further information is available at http://www.nsf.gov/pubs/2004/nsf04596/nsf04596.htm.


Gene-IT Joins SGI/Intel Program for 64-bit Migration

Bioinformatics firm Gene-IT is among 20 new software providers who have joined the Technical Computing Enabling Program (TCEP) — a joint effort between SGI and Intel designed to accelerate the migration of technical applications to from proprietary Unix systems to 64-bit Linux.

TCEP combines SGI’s Global Developer Program and Intel’s Early Access Program, and provides software developers with tools, expertise, resources, and technical roadmaps to migrate to 64-bit Linux.


University of Bonn Launches Master’s Course in Life Science Informatics

The University of Bonn in Germany said last week that it has begun to offer a two-year Master’s program in life science informatics.

The course, which is taught in English, will be offered together with the University of Aachen as part of the Bonn-Aachen International Centre for Information Technology under the overall control of the University of Bonn.

Applications are due by July 15. The university will accept 25 students for the course.

Further information is available at http://www.informatik.uni-bonn.de/III/bit/lsi/application/index.php.


Niagara University to Build a Bioinformatics Center

Niagara University said on June 29 that it has received $2 million in funding from the state of New York to build a new Center for Integrated Biological, Chemical and Technological Sciences.

“All the planning has been completed, and we are awaiting word from the state that we can begin drawing funds to purchase the necessary equipment,” said Joseph Levesque, university president, in a statement

Levesque added that $1.5 million is expected to be available from the state “shortly” to make the purchases. The university is providing $1 million in matching funds.

Niagara University has been designated a Center of Excellence under the state’s GenNYsis (Generating Employment through New York Science) program.

The university said it plans to build and equip four new labs for the center, which will focus on microscopic imaging, gene expression, biochemical molecular modeling, and tissue culture and protein purification.


The Scientist: New EMBL Director Sees Computational Methods as ‘Key’

Iain Mattaj, who was appointed as the next director general of the European Molecular Biology Laboratory last week, told The Scientist that broader use of computational methods across the European research laboratory system will be one of his top priorities when he takes the reins from the current director, Fotis Kafatos, next May.

Mattaj said that he aims to integrate quantitative methods into EMBL’s research processes. “The essential key is to incorporate computational methods into as many of our activities as possible,” he told The Scientist.


Fujitsu, Idenken to Co-Develop ‘World’s Fastest’ Database for DDBJ

Japan’s National Institute of Genetics, also known as Idenken, and Fujitsu said last week that they plan to co-develop a database for biological research that will be “the world’s fastest database system and position it as the de facto standard for the field,” according to a Fujitsu statement.

The system will be based on Fujitsu’s Interstage Shunsaku Data Manager Enterprise Edition XML database engine. The company said that a prototype for the system has achieved speeds 100 times faster than Idenken’s current database system.

The new system is expected to be installed at Idenken’s Center for Information Biology, which houses the DNA Data Bank of Japan, before the end of the year.

Fujitsu said that the Interstage Shunsaku database engine was originally developed for high-speed text searching, and that it has been enhanced to handle high-volume processing of complex data.


ViaLactia, Orion Donate Ryegrass Sequence Data to CSHL

ViaLactia Biosciences and Orion Genomics said last week that they will provide Cold Spring National Laboratory with data from their 2001 research alliance to characterize the ryegrass genome.

CSHL researchers will use the data to annotate publicly available plant sequences.

Results will be made available through the Gramene database (http://www.gramene.org).

Kieran Elborough, chief scientist of the forage genomics program at ViaLactia, described the database of proprietary genomic information as “an enormous collection of gene sequences” that has been “extensively studied using specifically developed bioinformatic tools” and “fully characterised using SAGE technology.”


Visualize and Insightful to Co-Market Life Science Software

Visualize and Insightful have entered into an agreement to jointly market their visualization and statistical analysis software in the life science and financial services industries.

“With Visualize, we are able to provide our customers with new ways to visualize data, and introduce and expand the reach of the S-Plus product family in key markets,” said Jeff Coombs, CEO of Insightful.

The companies said that they share “many common customers” in the life sciences and financial services markets.

Filed under

The Scan

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Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.