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Downloads & Upgrades: Apr 23, 2010


GenomeQuest has released GQ-PMR, a genomic reference system for personalized medicine-based research that is targeted at pharmaceutical companies who want to integrate raw data from public whole genome studies, such as the 1000 Genome Project, directly into their private research.

GQ-PMR includes three components: the aggregation, normalization, and hosting of raw public data; workflows that integrate this public data with private research data; and access to the GenomeQuest comparison engine and analysis tools.

The company said that researchers can use the system to verify rare variation hypotheses; scan targets against rare variant populations; find new associations for common diseases; stratify clinical test populations; and support genome-based diagnostics.

GenBank 177.0 is available via ftp from the National Center for Biotechnology Information.

Release 177.0 comprises approximately 114 gigabases and 119 million entries from non-WGS, non-CON sequences, and 165 gigabases and 58 million entries from WGS sequences.

Uncompressed, release 177.0 flat files require roughly 439 gigabytes for sequence files only. The ASN.1 data require approximately 361 gigabytes.

Accelrys has launched a Biological Registration application to help scientists register biological entities. The registration database has templates for yeast, cell lines, DNA, protein, plasmid, vaccine, antibodies, and siRNA with an "extensible knowledge model" and automated relationship cross-referencing to tailor the platform to the needs of a given group, the company said.

The firm said this software is the result of a three-year collaboration with several bio-pharmaceutical companies, including Abbott Laboratories and Merck.

The system can be accessed through standard desktop clients, web-based portals, or electronic lab notebooks, the company said.

IO Informatics said this week that it is now a certified partner under Dell's independent software vendor program and its Sentient software platform software suite is now validated under the program. This certification means that Dell has tested the software to assure its own standards for integration, IO said.

IO said that customers will be able to license its products through the Dell software and peripherals program.

Researchers at the University of Wisconsin-Milwaukee have launched Figure Search, which automatically searches for figures in full-text biomedical articles.

BASE 2.15 is available here.

The new release of the open source microarray database includes a new plug-in executor for running external analysis programs along with other features.

The University of California, Santa Cruz, has released a Genome Browser for the giant panda (Ailuropoda melanoleuca).

The assembly was produced by the Beijing Genomics Institute at Shenzhen. It comprises around 2.3 Gb at 94 percent coverage and includes 81,467 scaffolds.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or downloads page.

Specific conditions for use are available here.