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

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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.


Filed under

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.