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Downloads and Upgrades: Sep 10, 2010

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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

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.