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Genomic Workspace, Genomic Viewer, SRMS (Silico Regulation Management System), Human Genome Database, ProChart, UCSC Genome Browser, BioPAX, Bioinformatics Benchmark System, TurboWorx

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Rescentris has released the Genomic Workspace, a package to visualize, annotate, and edit sequence information in BSML format, along with the Genomic Viewer, a free, read-only version of the workspace. The package can be used to download and view sequence data from public databases, access BSML documents created by other users of the Genomic Workspace, and e-mail BSML documents to collaborators. The viewer is available at http://www.rescentris.com/products_viewer.html.


Silico Informatics Systems is offering a 30-day free evaluation version of its SRMS (Silico Regulation Management System) software for transcription factor binding site analysis from microarray data. SRMS uses results from MEME (Multiple Em for Motif Elicitation), MAST (Motif Alignment and Search Tool), and Gibbs algorithms, and can be integrated with Transfac to analyze sequences with experimentally determined binding sites. The evaluation software is available at http://www.silicoinformatics.com/SISWEB/download.htm.


Biomax has released version 3.1 of its Human Genome Database, which is integrated with AxCell Biosciences’ ProChart protein interaction data. The online database is available for $500 per user per year for academic and non-profit users, and $1,500 per user per year for commercial users. A demo version is available at https://ssl2.biomax.de/portal/HGRegistration/DemoRegistration.html.


The University of California Santa Cruz Genome Bioinformatics group has added Takifugu rubripes (fugu pufferfish) to the UCSC Genome Browser and Blat servers at http://genome.ucsc.edu. The assembly contains 20,379 scaffolds totaling 319 million base pairs.


The BioPAX consortium has released version 0.5 of BioPAX (Biological Pathways Exchange) Level 1, a pathway data exchange format, at http://www.biopax.org/ Download.html. The release is a preview of the format in order to generate discussion and feedback from the community, according to the BioPAX developers.


The Bioinformatics Benchmark System, an early version of a testing suite to permit performance comparisons of bioinformatics computing systems, is available at http://bioinformatics.org/bbs/. Current tests include several NCBI Blast runs. A database and scoring matrix are available on the download site in order to compare results.


TurboWorx has released three versions of its workflow collaboration technology for Mac OS X: TurboWorx Builder, TurboWorx Group, and TurboWorx Enterprise. TurboWorx’ framework also supports IBM AIX, Linux, Windows, Unix, and Solaris.

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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.