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Downloads and Upgrades: Ensembl 67, Cytoscape 2.8.3, Dotmatics’ Elemental for iPad, and More

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Ensembl release 67 is available here.

The release includes updates to the human genome assembly and the human somatic variants from Catalogue of Somatic Mutations in Cancer. It also includes a new species, Nile tilapia (Oreochromis niloticus) and updated assemblies for pig and squirrel


Cytoscape 2.8.3 is available here.

The release includes bug fixes and usability improvements including better support for Macs and reorganized plugin categories.

Cytoscape has also launched a beta release of the Cytoscape 3.0 application programming interface, which is intended to provide application writers with a solid foundation against which to port 2.X plugins or to build new apps.

Also available is version 2.5 of the GeneMania Cytoscape plugin and command line tools for gene function prediction.

This release contains bug fixes and no new features.


Dotmatics has released the first version of a free chemical drawing package, dubbed Elemental for iPad, which is available to download free from the iTunes App Store.

The tool lets users create, edit, and share chemical structures and reactions for either professional or educational use.


Omicia has begun an early-access program for its individual genome interpretation product, which will enable clinical researchers to prioritize and identify disease genes and their variants using a web-based application environment that includes the company’s Variant Annotation, Analysis and Search Tool, or VAAST, algorithm.

The early-access program will be available directly from Omicia as well as through third parties such as Illumina’s BaseSpace Apps.


The Protein DataBank website has been updated to provide domain-based protein structure alignments instead of chain-based alignments; improved search options such as the highlighting of search terms in the results list; and enhanced ligand summary reports.


The genome bioinformatics group at the University of California, Santa Cruz, has released browsers for the naked mole rat, Heterocephalus glaber, draft assembly; and the fugu, Takifugu rubripes, whole-genome shotgun assembly.


RefSeq 53 is now available from the National Center for Biotechnology Information via FTP.

This release incorporates genomic, transcript, and protein data available as of May 7, and includes 21,286,080 records, 15,744,232 proteins, 2,928,785 RNAs, and sequences from 17,339 different organisms.


Bowtie 2 2.0.0-beta 6 is available here.

The release handles longer reads in a more memory-economical fashion and fixes several software issues among other updates.


The Scan

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.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.