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Downloads and Upgrades Sep 30, 2011


Ingenuity Systems has launched Ingenuity iReport for Microarray Gene Expression, an integrated solution for statistical and biological interpretation of -omics data.

The software takes raw data as input and delivers a customized and interactive report that allows researchers to explore genes by function, biological process, role in pathway and disease, and cellular location.

Ingenuity said it will offer free early access to iReport to 5,000 researchers through Oct. 31.

The company said that future iReport offerings will focus on RNA-seq, qPCR, and other –omics platforms.

Velvet 1.1.06 is available here.

This release includes several bug fixes and an acceleration of the look-up table when running Columbus on large references.

The Protein Data Bank has launched a new structures widget.
The resource provides access to new PDB entries, related structure articles, and unreleased articles.

CLC Bio and Biobase have launched a free plugin that integrates curated biological databases contained in Biobase's Genome Trax with Genomics Gateway, CLC Bio's framework for visualizing, combining and analyzing genome data.

OpenMM 3.11 is now available here.

This version of the tool includes support for the AMOEBA polarizable force field and parallelization across multiple GPUs, plus other features.

Finnish bioinformatics company MediSapiens has released a comprehensive map of human gene expression for public use.

The data is available through a graphical tool called Transcriptome Viewer that lets users explore the expression activity of genes across chromosomes in several healthy human tissues.

Release 11 of Ensembl Genomes is available here.

The new release includes a migration to version 64 of the Ensembl software; cross-references to PHI-base, a database of pathogen-host interactions, added to genomes in Ensembl Protists; three new genomes in Ensembl plants; and other updates.

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.