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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

Just Breathing

A new analysis suggests that most Mycobacterium tuberculosis is spread by aerosols from breathing, rather than by coughing, the New York Times reports.

Just Like This One

NPR reports that the World Health Organization has hired a South African biotech company to recreate mRNA vaccine for SARS-CoV-2 that is similar to the one developed by Moderna.

Slow Start

The Wall Street Journal reports that Biogen's Alzheimer's disease treatment had revenues for July through September that totaled $300,000.

Genome Research Papers on Cancer Chromatin, Splicing in the Thymus, Circular RNAs in Cancer

In Genome Research this week: analysis of bivalent chromatin sites, RBFOX splicing factors' role in thymic epithelial cells, and more.