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Downloads and Upgrades: BioDatomics; RefSeq 50; Mosaic; iCTNet; TACC


This week, BioDatomics released a new version of its computational biology analysis and visualization platform.

According to the company, the combined software and hardware platform provides data storage and delivery capabilities and allows users to analyze, manipulate, visualize, and share data. It also includes a compression system that lets users move large volumes of data using a regular Internet connection.

RefSeq Release 50 is now available via FTP from the National Center for Biotechnology Information.

The full release incorporates genomic, transcript, and protein data available as of Nov. 7 and includes 18,815,153 records, 13,499,832 proteins, 2,751,095 RNAs, and sequences from 16,392 different organisms.

Two groups released new Cytoscape plugins this week.

A team at the Gladstone Institutes released a beta version of Mosaic, which is the first of a suite of Cytoscape applications that are being developed for annotating, analyzing, and visualizing networks with Gene Ontology terms. It partitions networks into subnetworks based on biological process terms; lays each one out using a cellular template based on cellular component terms; and then colors nodes based on molecular function terms.

Separately, a team in the University of California, San Francisco, neurology department released a plugin called the Integrated Complex Traits Networks, or iCTNet, which uses public information on gene expression, protein interaction, transcription factor binding sites, and drug targets to create multi-partite networks that can be used to study things like genetic similarities and differences across diseases, shared susceptibility pathways, and potential off-label use of FDA-approved drugs.

This week, the Texas Advanced Computing Center released an updated version of its computational biology software suite, which contains more than 30 new and updated applications for research in genomics, bioinformatics, and molecular simulation.

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