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Downloads and Upgrades May 13, 2011

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This week, GenoLogics released a version of its LIMS software that is pre-configured for Illumina's HiSeq and GA IIx sequencing systems and TruSeq sample prep kits.

The software includes new features that allow users to develop processes that map to Illumina's sample-preparation protocols and automate the calculation of dilution volumes for library normalization. It also offers views that are designed to simplify locating individual and pooled sequencing libraries that share similar sequencing requirements when loading flow cells.

On the sequencing side, a new dashboard lets users track the status of all Illumina sequencers in their labs, and track runs across multiple instruments. Users can populate the LIMS with key metrics, data location, and run status when a run is initiated on an Illumina sequencer. The tool also automatically creates sample sheets to support Casava 1.8 demultiplexing.


MolSoft has released iMolView, an application for iPhones and iPads that lets users browse protein, DNA, and drug molecules in 3D.

The app links directly to the Protein Data Bank and DrugBank. Users can zoom in and out, rotate, spin, pan, and clip the 3D molecules onscreen among other capabilities. Each molecular view can be customized with a set of molecular representations including: wires, balls-and-sticks, space filling, ribbon diagrams, and molecular surfaces.


Two Fold Software has made some changes to Qualoupe, its laboratory information management software solution.

Namely, the company has enhanced the interface design and user friendliness of the Run Manager software module of the LIMS to enable users to rapidly set up queues of samples to be processed through a specific laboratory instrument for a given method.


This week, Linguamatics released version 3.2 of I2E, its text mining software.

I2E 3.2 has reduced network bandwidth usage and faster interactive and batch querying. The updated version also includes a new word class that can be used as a linguistic wildcard in queries, and improved disambiguation to reduce unwanted hits among other new querying capabilities.


RefSeq Release 47 is now available via FTP from the National Center for Biotechnology Information.

The full release incorporates genomic, transcript, and protein data available as of May 7, 2011, and includes 17,631,876 records, 12,625,466 proteins, 2,619,015 RNAs, and sequences from 12,000 different organisms.


The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.