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Downloads & Upgrades: GQ-IP, GenBank 189.0, Cufflinks 2.0.0, Taverna Server and Taverna Workbench 2.4

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GenomeQuest has completed an integration agreement with online information services firm Questel that allows researchers to review biological sequence patents from GenomeQuest's GQ-IP system via Questel's Orbit platform, an IP database that includes tools for searching, mapping, watching, archiving, and sharing information.


The National Center for Biotechnology Information has released GenBank 189.0 via ftp.

Uncompressed 189.0 flatfiles require roughly 545 gigabytes for sequence files only or 586 gigabytes to include the short directory, index, and text files. The ASN.1 data requires approximately 446 gigabytes.


The University of Maryland Center for Bioinformatics and Computational Biology has released Cufflinks 2.0.0.

The new version of the RNA-seq analysis software "substantially improves the accuracy and robustness of differential analysis with Cuffdiff" and includes a large number of other enhancements. As a result, the developers said that it should be treated as a beta release.


The Taverna project has released Taverna Server 2.4 and the Taverna 2.4.0 Workbench and Command Line Tool.

The new version of Taverna Server supports multiple users; offers workflow run termination notifications through multiple mechanisms, including RSS feed, e-mail, SMS, and twitter; and includes improved security features.

New features in the Taverna Workbench include easier entry of large textual values, improved control over what is returned from REST services, and easier annotation of services.

The Command Line Tool allows users to execute workflows outside of Taverna Workbench and is available either as a stand-alone download or bundled with the Workbench.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.