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SRS 8.2, Ingenuity Pathways Analysis 4.0, IGB, DecisionSite, Ensembl 39, UCSC Genome Browser, GenBank 154.0, COPASI, DogBox Inside, Benchware Notebook 2.1, Dennis Rossi

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BioWisdom has released SRS 8.2, the first SRS update since BioWisdom acquired Lion Bioscience's bioinformatics business in April. SRS 8.2 is twice as fast for common indexing and querying tasks as previous versions, according to the company. The new version also offers improved data sharing and a simplified start page. The standard SRS package now includes SRS Relational, which allows users to combine and analyze internally generated databases with the third-party information supplied via SRS.


Ingenuity Systems has launched Ingenuity Pathways Analysis 4.0, which includes enhanced search and reporting capabilities. IPA 4.0 enables users to conduct and save advanced searches for genes, proteins, or biological relationships; create reports on bibliographies of pathway information; and export high-resolution images for publication and presentations. IPA 4.0 also supports the Mac platform in addition to PCs. Ingenuity is offering trials of the software at http://www.ingenuity.com/trial.


Affymetrix has released version 4.38 of IGB (Integrated Genome Browser), an application for visualizing genomes and annotations from multiple data sources, at http://www.affymetrix.com/support/developer/tools/download_igb.affx.


Spotfire has released analytic services for its DecisionSite software so that pharmaceutical scientists can visually analyze and interact with data from clinical trials. Features include integration with customer clinical data management and electronic data capture systems, support for SAS files and programs, and guided analyses for quality control and monitoring of clinical data.


Ensembl 39 is available at http://www.ensembl.org. The release includes new assemblies for mouse, zebrafish, opossum, and Ciona savignyi and other updates.


The Genome Bioinformatics Group at the University of California, Santa Cruz, has released version 4.1 of the Xenopus tropicalis assembly through the UCSC Genome Browser at http://genome.jgi-psf.org/Xentr4/Xentr4.home.html and a Genome Browser for the v3.4 Rattus norvegicus genome at ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/ or http://hgdownload.cse.ucsc.edu/downloads.html#rat.


The National Center for Biotechnology Information has released GenBank 154.0 at ftp://ftp.ncbi.nih.gov/. The release contains 63,412,609,711 base pairs and 58,890,345 entries. Uncompressed, the 154.0 flat files require about 222 GB for the sequence files only. The ASN.1 version requires around 192 GB. NCBI said that a new protein residue abbreviation for the 22nd amino acid, pyrrolysine, will become "legal" in GenBank protein sequences as of release 156.0, in October. "Because several letters are assigned to represent different experimental ambiguities, the only letter still available for use is O (uppercase letter o)," NCBI said. For Blast and other sequence similarity search tools, NCBI said it will map pyrrolysine (O) to unknown (X), as it already does with selenocysteine (U), the 21st encoded amino acid. The 156.0 release will also include the residue abbreviation J for leucine/isoleucine ambiguities in mass spectrometry experiments. "Although this abbreviation has been part of the IUPAC recommendations for some time, it has not previously appeared in protein sequences in the GenBank database," NCBI said.


EML Research and the Virginia Bioinformatics Institute have launched COPASI (Complex Pathway Simulator), a software package that allows users to model, simulate, and analyze biochemical and systems biology networks, at http://www.copasi.org.


Unleashed Informatics has launched DogBox Inside, a remotely maintained data warehouse that is installed on the customer's in-house hardware and open to customer audit and compliance requirements. DogBox Inside includes hourly updated gene sequence and molecular interaction data from 18 sources, as well as pre-computed BlastP and RPS-Blast information for all protein sequences in NCBI's NR database. The service is priced at $14,500 per year.


Tripos has released Benchware Notebook 2.1, an update of its enterprise electronic laboratory notebook. The new version includes a new page navigation toolbar and increased support for third-party chemical sketching applications.

People in the News

Dennis Rossi, has resigned as senior vice president and general manager of genomics at Gene Logic (see briefs, this issue). Rossi joined the company in 2004. Prior to that, he served as vice president of marketing for life sciences for Accelrys and was a partner for Harvard Strategy Group, a life sciences consulting firm. He also held several senior level management positions at Digital Equipment Corporation, which was acquired by Compaq (now Hewlett-Packard).

Filed under

The Scan

Review of Approval Process

Stat News reports the Department for Health and Human Services' Office of the Inspector General is to investigate FDA's approval of Biogen's Alzheimer's disease drug.

Not Quite Right

A new analysis has found hundreds of studies with incorrect nucleotide sequences reported in their methods, according to Nature News.

CRISPR and mRNA Together

Time magazine reports on the use of mRNA to deliver CRISPR machinery.

Nature Papers Present Smartphone Platform for DNA Diagnosis of Malaria, Mouse Lines for Epigenomic Editing

In Nature this week: a low-cost tool to detect infectious diseases like malaria, and more.