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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

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.