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Downloads and Upgrades: PubmiR, Cytoscape 3.0, DNAnexus, and more.


This week, Firefly BioWorks released PubmiR, a free search engine for microRNA pathways.

The tool uses proprietary algorithms to search for information about microRNAs in miRBase v19 and PubMed databases based on search criteria such as disease conditions and organism. It then ranks relevant microRNA species according to their frequency of occurrence in underlying journal articles.

Cytoscape 3.0 is available here.

The release includes new data table controls, integrated support for graphical annotations in networks, and an improved architecture and application programming interface among other new features.

This week, Accelrys said that its customers can now access Elsevier's Reaxys, a discovery engine for chemistry, directly from Accelrys Electronic Laboratory Notebook.

The company said that the integration will help users search and retrieve information about chemical reactions, substances, and related property data faster and more efficiently.

Elsevier has launched Reaxys Medicinal Chemistry, a tool that gives medicinal chemists access to experimental data on druggable targets, pharmacological effects, biological data points, and ADME properties associated with chemical compounds.

DNAnexus has launched a beta version of its new cloud-based analysis platform.

The company said that its new platform's features include a configurable command line interface and a genomics toolbox that lets users run Linux tools as well as develop custom programs using APIs and software development kits for Python, C++, and other languages.

This week, Softberry released several free bioinformatics applications for academic users.

These include applications for analyzing RNA-sequencing data, de novo assembly, and a software package for SNP data. The firm is also offering programs for genome alignment, bacterial and eukaryotic promoter prediction, functional/regulatory motifs discovery, splice sites identification, gene prediction, and tools for protein sequence and structure analysis.

Biopython 1.61 is available here.

The release includes improvements to existing modules and the addition of a new module, Bio.Graphics.ColorSpiral, which can generate colors along a spiral path through the HSV color space, among other updates.

Release 17 of Ensembl Genomes is available here.

This release includes more than 6,000 newly added bacterial genomes. Also, the developers have added new genomes to Ensembl fungi and Ensembl protists, and made improvements to some existing genomes among other updates.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.