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Downloads and Upgrades Aug 26, 2011

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Decodon has released Delta2D 4.3

According to the developers, the latest release includes improvements in quality control and statistical tests, complete expression profiles for heterogeneous projects with its new Connector tool, and improved automatic warping among other features.


BioDiscovery has released Nexus Copy Number 6.0, the latest version of its software for DNA copy number analysis from CGH and single nucleotide polymorphism array data.

This version of the tool incorporates the Genomic Identification of Significant Targets in Cancer, GISTIC, algorithm for identifying regions of common genomic abnormalities and the Allele-Specific Copy Number Analysis of Tumors, ASCAT, algorithm which addresses sample aneuploidy and mosaicism, among other updates.


This week, Kinexus Bioinformatics launched the TranscriptoNET KnowledgeBase, an open access resource that provides human gene expression data from more than 300 types of human tissues and organs as well as more than 300 human cancer cell lines.

The tool includes information from the National Center for Biotechnology Information's Gene Expression Omnibus on mRNA expression levels for nearly 23,000 human genes to help users discover genes that are uniquely or commonly expressed in the human body, as well as interactions between proteins based on co-expression patterns.


Developers at the Joint BioEnergy Institute have made several changes to j5, the institute's automated DNA assembly software.

The software now features an improved graphical design canvas that improves its usability and accessibility. It is also better integrated with the JBEI sequence repository database platform and with liquid-handling robotics. For instance, it can design the arrangements of PCR reactions in 96-well plates across thermocycler gradients, JBEI said.


The Scan

Looking for Omicron

NPR reports that SARS-CoV-2 testing in the US has gotten better but also that some experts say more needs to be done to better track the Omicron variant.

Holmes Alleges Abuse

The Associated Press reports that Theranos' Elizabeth Holmes has testified at her wire fraud trial that her business and romantic partner abused her.

Bit More Diverse, But More to Do

While Black and Hispanic patients are more likely to participate in cancer clinical trials than previously, they are still underrepresented, according to US News & World Report.

PNAS Papers on Yeast Gene Silencing, Zika Virus Inhibition, Immunoglobulin Hypermutation

In PNAS this week: gene silencing in Saccharomyces cerevisiae, possible neuroprotective role for SHFL in a mouse model of Zika virus infection, and more.