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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

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.

Seagull Microbiome Altered by Microplastic Exposure

The overall diversity and the composition at gut microbiome sites appear to coincide with microplastic exposure and ingestion in two wild bird species, according to a new Nature Ecology and Evolution study.

Study Traces Bladder Cancer Risk Contributors in Organ Transplant Recipients

In eLife, genome and transcriptome sequencing reveal mutation signatures, recurrent somatic mutations, and risky virus sequences in bladder cancers occurring in transplant recipients.

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.