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Magelan, HDFR, GOtcha, UCSC Genome Browser, BioPAX, VEGA ZZ 2.0.0, HapMap, ChemStation

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Incogen has released desktop versions of its Magelan gel analyzer and HDFR (high-density filter reader) software packages. Both products are priced at $995 for a perpetual license.


GOtcha, a software tool for assigning Gene Ontology terms based on sequence similarity searches to annotated genomes, is available from the University of Dundee at http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html. GOtcha provides graphical output that provides confidence measures for GO term assignments.


The University of California Santa Cruz Genome Bioinformatics Group has released version 3.0 of the Xenopus tropicalis assembly through the UCSC Genome Browser. The whole-genome shotgun assembly, which totals 1.63 Gbp, was provided by the US DOE Joint Genome Institute and was constructed with JGI’s Jazz assembly algorithm. More information about the assembly is available at http://genome.jgi-psf.org/Xentr3/Xentr3.home.html.


The BioPAX Workgroup has released BioPAX Level 1, version 1.2, in OWL (Web Ontology Language). The release of the pathway data-exchange format represents metabolic pathways and also provides additional support for description logic reasoning and is available at http://www.biopax.org.


Milan’s Istituto di Chimica Farmaceutica e Tossicologica has released VEGA ZZ 2.0.0 at http://users.unimi.it/~ddl/vega/. The new version of the molecular modeling software package offers several new features, including increased computational speed, a new graphical interface, fast solid and mesh surface calculation and multiple surface management, the ability to add amino acid side chains, and enhanced image-rendering capabilities.


HapMap data release 13 is now available from the HapMap Data Coordination Center at Cold Spring Harbor Laboratory at http://www.hapmap.org. The release includes genotypes from all four HapMap populations: 856,726 SNPs genotyped in CEPH, 386,323 SNPs in Han Chinese, 386,274 SNPs in Japanese, and 406,783 SNPs in Yoruba.


Agilent has released a 32-bit version of its ChemStation instrument-control and data-management software (version B.01.01). According to Agilent, the 32-bit architecture improves the software's performance and stability. Agilent has also released revision B.03.02 of its ChemStore and ChemStation Plus Security Pack add-on software modules to provide support for the 32-bit ChemStation.

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The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.