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Nexus CGH, I2E 2.10, Definiens Enterprise Image Intelligence Suite 7, OmicBrowse, EMBOSS 5.0.0, UCSC Genome Browser

BioDiscovery has released Nexus CGH, a tool for analyzing array CGH-based data from Agilent, Nimblegen, Affymetrix, Illumina, Empire Genomics, and most home-spotted arrays. According to the company, Nexus CGH can support large-scale array CGH-based experiments involving hundreds of samples from any platform, including high-density Agilent 244K arrays as well as Nimblegen’s 3-million-probe tiling arrays. The software is currently only available through the company’s early-adopter program. It runs on OS X, Windows, and Linux.

Linguamatics has released I2E 2.10, the latest version of its natural language processing software. Enhancements include new querying capabilities, including extraction and analysis of quantitative information; improved results output options, including XML output and visualization of interaction networks; more effective mining of full-text articles and patents; improved capabilities for streamlining and automation; and improved management and use of custom-built and off-the-shelf ontologies.

Definiens has released the Definiens Enterprise Image Intelligence Suite 7, a new version of its image-analysis platform that includes enhanced data-management capabilities. Features in the new release include improved viewing and visualization tools, such as multi-magnification views and heatmaps; a new graphical environment that allows scientists to configure their own applications; a new web-based administrator; and improved integration capabilities.

Japan’s RIKEN has released an update for the OmicBrowse genome browser, which displays an integrated view of multiple omics annotations filtered with ontologies. New functions include access controls over secure datasets, the ability to change the browser's window size, and genome annotations for human, mouse, rat, C. elegans, Arabidopsis, and rice. 

EMBOSS 5.0.0 is available here. The Windows version is now called mEMBOSS and installs with a standalone version of Jemboss as a GUI. It is available here.  

The Genome Bioinformatics Group at the University of California, Santa Cruz, has made the latest Drosophila melanogaster assembly available through the UCSC Genome Browser. The assembly, Release 5 (UCSC version dm3), was provided by the Berkeley Drosophila Genome Project and combines both euchromatic and heterochromatic sequence. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Genome Browser downloads page.

Nucleic Acids Research has published its annual web server issue, which includes 130 papers describing web-based computational tools for analyzing DNA, RNA, and protein sequences and structures. “A handful of theseare updates to existing web servers, but the overwhelming majorityare new resources,” according to an editorial in the issue, which is freely available here. A complete listing of the 2005 NAR servers is available here

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The Scan

Harvard Team Report One-Time Base Editing Treatment for Motor Neuron Disease in Mice

A base-editing approach restored SMN levels and improved motor function in a mouse model of spinal muscular atrophy, a new Science paper reports.

International Team Examines History of North American Horses

Genetic and other analyses presented in Science find that horses spread to the northern Rockies and Great Plains by the first half of the 17th century.

New Study Examines Genetic Dominance Within UK Biobank

Researchers analyze instances of genetic dominance within UK Biobank data, as they report in Science.

Cell Signaling Pathway Identified as Metastasis Suppressor

A new study in Nature homes in on the STING pathway as a suppressor of metastasis in a mouse model of lung cancer.