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Downloads & Upgrades: Reactome 39; GenBank 187.0; EMBL-Bank 110; Velvet 1.2.01; and more


Reactome 39 is available here.

The release includes a new disease topic that contains HIV, influenza, botulinum neurotoxicity, amyloids, and diabetes pathways, as well as an EGFR signaling pathway in cancer. Topics with new or revised events in this release include immune system, metabolism, signal transduction, and gene expression.

The National Center for Biotechnology Information has released GenBank 187.0 via ftp.

Uncompressed187.0 flatfiles require roughly 518 gigabytes for sequence files only or 557 gigabytes to include the short directory, index, and text files. The ASN.1 data requires approximately 426 gigabytes.

This week, the genome browser team at the University of California, Santa Cruz, said that the UCSC Genome Browser now supports the Variant Call Format — an extendable line-oriented text format developed by the 1000 Genomes Project for releases of single nucleotide variants, indels, copy number variants, and structural variants.

Release 110 of the European Nucleotide Archive/EMBL-Bank is available from the European Bioinformatics Institute's ftp servers and other mirror sites.

Full release notes are available here.

Velvet 1.2.01 is available here.

This release includes a performance enhancement for users who are running Velvet on large datasets.

Version 2.3 of the GeneMania Cytoscape plugin and command line tools is now available.

This release includes numerous bug fixes; support for importing custom organisms into datasets; and the ability to create groups when importing networks, among other features. The tool also includes an improved linear system solver in the GeneMania algorithm.

Version 1.10 of the open source software UGENE has been released.

The latest version of the tool features several new tools including MrBayes and BWA; updates to Bowtie and Blast tools; improvements to the short-read assembly viewer; and new data filtering elements.

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