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Phenyx, GENSAT, RefSeq8, NCBI Map Viewer, Dymension, FlyBase, Argo, CDMS, DMS

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Geneva Bioinformatics has released a 30-day trial version of Phenyx, its software platform for the identification of proteins and peptides from mass spectrometry data. Both the trial and the full versions of the software are available at http://www.phenyx-ms.com/downloads/downloads.html.


The National Center for Biotechnology Information has announced several resource updates: The GENSAT (Gene Expression Nervous System Atlas) database has been incorporated into the Entrez system (http://www.ncbi.nlm.nih.gov/projects/gensat/); RefSeq8 is available (at ftp://ftp.ncbi.nih.gov/refseq/release/), and includes 1,218,266 proteins and sequences from 2,645 organisms; build 1, version 1 of the Pan troglodytes (chimpanzee) genome is now available from the NCBI Map Viewer (at http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9598); and Ciona savignyi (sea squirt) has been added to UniGene (at http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?db=unigene).


Syngene has launched Dymension, a 2D gel software package that can analyze a typical 2D gel image “in seconds,” according to the company. Dymension also includes a new spot-finding algorithm that enables minimal post-editing.


The FlyBase Drosophila genome database has recently released Drosophila melanogaster (Dmel) 4.0 and Drosophila pseudoobscura (Dpse) 1.0 at ftp://flybase.net/genomes/Drosophila_melanogaster/current/ and ftp://flybase.net/genomes/Drosophila_pseudoobscura/current/. The Dmel release includes 13,472 genes among a total of 1,330,192 curated, matched and predicted features. The Dpse release includes 12,197 predicted genes with orthologous matches to Dmel genes, among 228,876 total genomic features.


The Broad Institute has released Argo, the genome browser for the Calhoun annotation system, at http://www.broad.mit.edu/annotation/argo. Argo, a Java application for manually annotating whole genomes, was developed for Broad Institute researchers analyzing the human genome.


Biotrue has released CDMS (Collaborative Data Management System), a software system for capturing, storing, managing and retrieving biomedical research data. The company said that CDMS differs from other data management products, such as LIMS, because it can handle data “from virtually any type of instrument, and, as a Web-enabled application, facilitates easy and secure collaboration within and across laboratories.”


iAdvantage Software has released DMS (Data Management System), a web-basedsoftware product for collecting and reporting life science data. The DMS platform comprises three components: Design and Management; Web Data Collector; and Document Generator.

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The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.