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Downloads and Upgrades: Jun 3, 2011

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The Center for Bioinformatics and Computational Biology at the University of Maryland has released TopHat 1.3.0.

The new version of the spliced read mapper for RNA-seq data includes a restructured internal workflow that compresses all temporary data during a run in order to improve running time on networked filesystems.

The software now supports both GTF2 and GFF3 formats and can take gzip or bzip2 compressed FASTQ or FASTA files as input


Japan's Riken has released a new web service interface, called Semantic-JSON, to provide investigators with access to life science research data across multiple public and private domains.

The interface accesses a "virtual laboratory cloud center" named the Scientists' Networking System, which brings together 192 public database projects and provides access to data records and a network of semantic relationships.

The tool lets users access data from across the SciNetS network using the programming languages and information tools they normally use in their research by defining a set of simple but relevant commands for accessing and searching SciNetS data and their semantic relationships and delivering results in the JavaScript Object Notation format.

A paper describing the tools was published in a recent issue of Nucleic Acids Research.

The Scan

Push Toward Approval

The Wall Street Journal reports the US Food and Drug Administration is under pressure to grant full approval to SARS-CoV-2 vaccines.

Deer Exposure

About 40 percent of deer in a handful of US states carry antibodies to SARS-CoV-2, according to Nature News.

Millions But Not Enough

NPR reports the US is set to send 110 million SARS-CoV-2 vaccine doses abroad, but that billions are needed.

PNAS Papers on CRISPR-Edited Cancer Models, Multiple Sclerosis Neuroinflammation, Parasitic Wasps

In PNAS this week: gene-editing approach for developing cancer models, role of extracellular proteins in multiple sclerosis, and more.