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Downloads and Upgrades: Sep 10, 2010


The GeneMania prediction algorithm is now available as a plugin for Cytoscape versions 2.6.2+ and 2.7.0+.

Among other features, the algorithm lets users perform fast gene function predictions using a dataset comprised of more than 800 networks containing 181 million interactions for six model organisms. Users can also perform predictions using their own data by importing interaction networks and expression profiles and the plugin automatically transforms the results into a Cytoscape network for further analysis.

Users need at least 4 gigabytes of RAM to perform predictions using the default networks, and at least 6 gigabytes when using all networks.

Additional details including installation instructions are available here and the plugin can be downloaded here under the network inference category.

Biopython version 1.55 is available here.

In this release, the command line tool application wrapper classes are now executable making it easier to call external tools, GenBank and EMBL parsing is faster, BioSQL classes function more like Python dictionaries, and Bio.PDB handles model numbers and missing element columns better.

The developers also announced that while they are phasing out support for version 2.4 of the python programming language, they will include it in Biopython 1.56

The Scan

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Officials in the UK say the B.1.617.2 variant of SARS-CoV-2 may be as transmitted as easily as the B.1.1.7 variant that was identified in the UK, New Scientist reports.

Gene Therapy for SCID 'Encouraging'

The Associated Press reports that a gene therapy appears to be effective in treating severe combined immunodeficiency syndrome.

To Watch the Variants

Scientists told US lawmakers that SARS-CoV-2 variants need to be better monitored, the New York Times reports.

Nature Papers Present Nautilus Genome, Tool to Analyze Single-Cell Data, More

In Nature this week: nautilus genome gives peek into its evolution, computational tool to analyze single-cell ATAC-seq data, and more.