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Downloads and Upgrades: GenBank 200.0, Entrez Direct, Nexus Copy Number software, and more


GenBank 200.0 is now available from the National Center for Biotechnology Information via ftp.

Uncompressed flatfiles in this release require roughly 625 gigabytes for sequence files only. The ASN.1 data require approximately 522 GB.

The NCBI has also released Entrez Direct, a new software suite that lets researchers use the UNIX command line to directly access NCBI’s data servers, as well as parse and format data to create customized data files; and version 3.11 of the Conserved Domain Database which includes recomputed position-specific score matrices and uniform display styles among other updates.

OpenEye Scientific Software has released OpenEye Toolkits v2014.Feb.

This release adds two new toolkits to the collection namely; Szmap TK, which provides access to the core functionality used by the SZMAP application and enables the calculation of solvent energies and probabilities at arbitrary points in space, and OEMedChem TK, which provides many useful tools that have been requested by users. There are also improvements to existing features as well as bug fixes.

BioDiscovery has released version 7.5 of the Nexus Copy Number software, its platform for analyzing sequence and structural variation data from microarray and NGS platforms.

This version of the software includes a new NGS module for analyzing sequence variants from array or NGS platforms, and for detecting copy number variants from sequencing data. It also includes expanded support for the Affymetrix platform with support for the OncoScan FFPE Assay Kit and Affymetrix Axiom Human Genotyping array among other updates.

The Broad Institute has released GenePattern 3.8.0.

Features in this release include an updated user interface, the ability to run a batch job over multiple dragged in files, pipeline designer improvements, bug fixes, and more.

Cytoscape v 3.1.0 is available here.

New features in this release include a greatly improved vizmapper, an improved welcome screen, annotation groups, app citation listings, updated user documentation and more.

The Scan

Taking Stock of the Stockpile

The US and European countries are evaluating their smallpox vaccine stockpiles as the number of monkeypox cases increases, the Washington Post reports.

Vitamin D From Tomatoes

According to Reuters, researchers in the UK have gene-edited tomatoes so their fruit contains vitamin D.

Cause Not Yet Spotted

NPR reports that a new study was unable to find a cause for persistent long COVID symptoms.

PNAS Papers on Central African Hunter-Gatherers, Myopia Development, Ancient Microtia Allele

In PNAS this week: population patterns among Central African hunter gatherers, effect of myopia-linked gene variant, and more.