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Genotyping Console 2.0, GeneMarker, Gemini, Taverna 1.7.0, BioRuby 1.2.0, BIRCH 2.3

Affymetrix has released Genotyping Console 2.0, a software tool for determining SNP genotypes and chromosomal copy number changes in whole-genome association and cytogenetic studies. GTC 2.0 works with the company’s Genome-Wide Human SNP Array 6.0. Affymetrix said that the software offers researchers “up to 10 times the sensitivity for detecting copy number changes than competing platforms.”
GTC 2.0 displays and organizes all the data from the SNP Array 6.0, which includes more than 1.8 million markers. The software includes new algorithms and new visualization and reporting tools.

SoftGenetics has released a new version of its GeneMarker software that includes a new analysis and reporting module for use with MRC Holland’s Methylation-Specific Multiplex Ligation-dependent Probe Amplification kits. The MLPA method is used to detect genomic imprinting diseases such as Prader-Willi syndrome and Angelman syndrome.
The company said that the new MS-MLPA module “quickly and accurately detects methylation sites for researchers studying promoter methylation and genomic imprinting diseases.”
A free 30-day trial of GeneMarker is available here.

The National University of Singapore has released the Gemini suite of gene expression mining tools. The suite includes Carpenter, a pattern-mining algorithm for analyzing tables with a large number of columns (10,000-100,000) and a small number of rows (200-1,000); TopkIRG, a rule-extraction and classifier construction algorithm; and RegMiner, a gene-clustering algorithm.


Taverna 1.7.0 is available for download here.
The release includes a “technology preview” of Taverna 2 in the form of a plug-in that can translate and run a Taverna 1 workflow. Taverna 1.7 also includes BioMoby improvements and plug-in extension points.

BioRuby 1.2.0 is available here.
The new release includes improvements to the BioRuby shell and enhancements to the Bio::Blast, Bio::PubMed, Bio::FlatFile, Bio::KEGG::COMPOUND, and Bio::KEGG::API modules.

The Department of Plant Science at the University of Manitoba has released BIRCH (Biological Research) 2.3 here. BIRCH includes freely available programs and databases for molecular biology.

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The Scan

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.

Study Presents New Insights Into How Cancer Cells Overcome Telomere Shortening

Researchers report in Nucleic Acids Research that ATRX-deficient cancer cells have increased activity of the alternative lengthening of telomeres pathway.

Researchers Link Telomere Length With Alzheimer's Disease

Within UK Biobank participants, longer leukocyte telomere length is associated with a reduced risk of dementia, according to a new study in PLOS One.

Nucleotide Base Detected on Near-Earth Asteroid

Among other intriguing compounds, researchers find the nucleotide uracil, a component of RNA sequences, in samples collected from the near-Earth asteroid Ryugu, as they report in Nature Communications.