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Downloads and Upgrades: Jan 21, 2011

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The Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, launched version 1.9 of structureViz, a Cytoscape plugin that provides an interface between Cytoscape and UCSF's Chimera.

Features in this release let users find hydrogen bonds between and within structures, detect clashes between structures, load SMILES structures, search for modeled structures using Modbase, and provide a relatively complete set of CyCommands to expose structureViz functionality to other plugins, or to support scripting.


TopHat 1.2.0 is now available.

According to the developers, the latest version of the splice junction mapper for RNA-seq reads includes important bug fixes, detects insertions and deletions, reports reads aligned across indels by taking advantage of I and D CIGAR operators as specified by the SAM format, corrects issues with aligning reads of mixed lengths, and has improved runtime validation for input files.


This week, Waters launched the Waters Biopharmaceutical System Solution.

According to a release, the system brings together Waters UltraPerformance Liquid Chromatography mass spectrometry technology and bioinformatics technologies to provide a solution that unites all aspects of biotherapeutic analyses and workflows; and results in a system that conforms to biopharmaceutical quality guidelines and regulations.

The company said that the system includes its Acquity UPLC H-Class Bio System; Waters Peptide and Protein Separation Technology Columns; Xevo G2 Tof Mass Spectrometer; and the Unifi Scientific Information System.

These tools provide a solution that implements UPLC, exact-mass Tof MS, and bioinformatics technologies that are built for biotherapeutic analysis, addresses protein characterization needs, and streamlines analytics by standardizing workflows across laboratories, among other features.


Linguamatics has launched I2E OnDemand, the cloud version of its I2E text-mining platform.

The product features the natural language programming-based querying capabilities of the enterprise version of I2E and will be provided with a range of different vocabularies and ontologies. According to the company, I2E OnDemand is being launched initially for use with Medline.


The Genome Browser team at the University of California, Santa Cruz, has added the latest zebrafish assembly as danRer7.

The assembly, which was produced by the Wellcome Trust Sanger Institute, is available here.


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.