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CGH Analytics, caCORE, Oracle Spatial Network Data Model, RefSeq 9, BioRS, Rosetta Resolver, Reactome, SkyPainter2, HIC-Up

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Agilent Technologies last week launched its Human Genome CGH Microarray and CGH Analytics software. The software provides simultaneous visualization of multiple CGH microarray profiles, statistical measures to detect aberrant regions, and other features.


The National Cancer Institute’s Center for Bioinformatics has released the caCORE Software Development Kit, a set of tools that can be used to create a software system designed using a model-driven architecture; an n-tier architecture with open APIs, controlled vocabularies, and registered metadata. The SDK is available under an open source software license at http://ncicb.nci.nih.gov/core/SDK.


Oracle has released the Oracle Spatial Network Data Model plug-in for the Cytoscape network analysis platform at http://cytoscape.org/plugins2.php. The plug-in allows Cytoscape users to visualize and analyze network data stored in Oracle Spatial Network Data Model.


The National Center for Biotechnology Information has released build 1, version 1, of the Canis familiaris (dog) genome assembly at http://www.ncbi.nlm.nih.gov/genome/guide/dog/. NCBI has also released RefSeq 9, which includes 1,310,899 proteins and sequences from 2,780 different organisms, at http://www.ncbi.nlm.nih.gov/projects/RefSeq.


Biomax Informatics has launched version 5.4 of the BioRS Integration and Retrieval System, which provides access to public and proprietary data in a distributed environment.


Rosetta Biosoftware has integrated the Affymetrix GeneChip Operating Software with version 5.0 of Rosetta Resolver. The company said that the integrated system will enable advanced interpretation of results from Affy arrays.


Version 12 of Reactome is available at http://www.reactome.org. The release includes three new modules: mitotic spindle checkpoint, protein translation termination, and the first stage of xenobiotic metabolism. The Reactome project has also released a tool called SkyPainter2, which allows users to overlay protein or gene identifiers on the reaction map or visualize microarray data.


An updated version of HIC-Up (Hetero-compound Information Center, Uppsala) is available from the University of Uppsala at http://xray.bmc.uu.se/hicup/release.html. The database now contains information on 5,384 small molecules from the Protein Data Bank (up from 4,968), along with several other new features.

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The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.