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GeneMarker, Bioconductor 1.9, BONDplus, ImaGene aCGH, CESE 1.4.5, CMVE, MDL Notebook

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SoftGenetics has released a new module for its GeneMarker software for MLPA (multiplex ligation-dependent probe amplification) analysis using Luminex xMap technology. The software, developed in collaboration with the Mayo Clinic and Foundation, detects exon copy number changes associated with breast and colon cancers, as well as trisomies found in Down syndrome. GeneMarker Luminex-MLPA automatically performs background subtraction and flags suspect intensities according to user-specified thresholds, the company said. The software selects the least variable sample from the sample set to act as the reference for determining copy number change.
 

 
Bioconductor 1.9 is available here. The release includes 26 new packages and improvements to existing packages. Bioconductor 1.9 is compatible with R 2.4.0, which was released here on Oct. 3. New packages include ABarray for QA and statistical data analysis for the Applied Biosystems array platform, beadarraySNP for normalizing and reporting Illumina SNP bead arrays, iSNetwork for interactive network plots, sigPathway for pathway analysis, and pcaMethods, which is a collection of methods for principal components analysis.
 

 
Unleashed Informatics has launched BONDplus (the Biomolecular Object Network Databank). BONDplus is a life science data-management platform that combines sequence and interaction information. Subscribers to the software can conduct Blast queries against both sequence and interaction data within a common interface. The company plans to further extend the platform to include cheminformatics, patents, and publication information. Subscriptions to BONDplus Online start at $1,850 for academics.
 

 
BioDiscovery has released ImaGene aCGH (array Comparative Genomic Hybridization), a software module for its ImaGene 7.0 microarray analysis platform that enables researchers to analyze, normalize, and visualize DNA gains and losses.
 

 
The Department of Plant Science at the University of Manitoba has released BIRCH (Biological Research) 2.0 here. BIRCH includes freely available programs and databases for molecular biology.
 

 
CESE (Cell Electrophysiology Simulation Environment) 1.4.5 is available here. CESE is an integrated environment for performing computational simulations using a variety of electrophysiological models. The new release is based on Java 1.5 and includes features to improve the stability of multithreaded code.
 

 
The CMVE (collateral missing value estimation) toolbox, which estimates missing values in microarray data and other correlated data sets, is available from MonashUniversity here. CMVE imputes missing values in the correlated data in order to improve the accuracy of gene regulatory network modeling, class prediction, gene selection, clustering, and other analysis methods, according to its developers.
 

 
Elsevier MDL has released MDL Notebook, an electronic laboratory notebook built on the company’s Isentris system. MDL Notebook is integrated with MDL’s Available Chemicals Directory sourcing database, the MDL Logistics reagent management system, the MDL Registration system, and DiscoveryGate content platform.

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The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.