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Downloads and Upgrades: Jun 24, 2011

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The Open Microscopy Environment Consortium has released a beta version of OMERO 4.3.0.

The software now supports large, tiled images from Aperio, NanoZoomer, and other imaging systems, and includes improvements to client applications.


Real Time Genomics has released a free version of RTG Investigator 2.2, its sequence analysis software for variant detection and metagenomic analysis.

The software currently supports data from Illumina, Complete Genomics, and Roche 454 sequencers and uses proprietary algorithms for advanced variant detection and metagenomic analysis, the company said.

The tool lets users map overlapping, gapped reads from Complete Genomics and provides a translated nucleotide search pipeline that includes contaminant filtering, metabolic function definition, species estimation, and similarity analysis among other capabilities.


Exiqon has released a new version of its qPCR data analysis software.

The tool includes a new data import wizard that enables automatic annotation of different miRNA assays and direct import of instrument data files. The software also supports batch-mode analysis of several hundred data files and incorporates Exiqon’s quality control assays. It also lets users perform multiple statistical analyses such as t-tests, advanced principal components analysis, and heat map plots, as well as retrieve database information from resources such as miRBase, miRtarget, miRtissue, and others.


Cambridge University Press has published three guides to the EMBOSS suite of bioinformatics tools: the EMBOSS Administrator's Guide, which provides information about software management; the EMBOSS Developer's Guide, which provides details about bioinformatics programming; and the EMBOSS User's Guide, which provides details on practical bioinformatics.


Researchers at the Center for Biomedical Informatics at Children's Hospital of Philadelphia have launched Genome Wowser, a free iPad app for exploring genomic information.

Likening the tool to Google Maps, the developers said it enables interacting browsing of the human genome, including functional annotations.

Genome Wowser supports viewing and querying of multiple types of genomic data, so that users can select the types of information that interest them and view them concurrently in a stacked display for a selected region. In addition to text-based and graphical search options, the app provides zooming capabilities and drag-and-swipe navigation.

Upcoming versions of the app will provide access to genome sequences of more than three dozen non-human species, including dogs, cats, mice, chimpanzees, elephants, and 11 species of fruit fly, plus further improvements in the touch interface.


Reactome 37 is available here.

New topics include a new pathway topic on amyloids and several revised events including synaptic transmission, metabolism of amino acids and derivatives, and RNA metabolism.


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.