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Downloads and Upgrades: Labguru, LibraryView, Vortex, Velvet 1.2.08, and more


BioData, a scientific software service company, has added more than 30 Luminex multiplexing protocols to Labguru, its web-based lab management application.

According to the company, when researchers add a protocol to their Labguru accounts, its steps and procedures are automatically included and each protocol can be copied and adapted for use in different experiments. Furthermore, associated kits, reagents and materials are also automatically added to the account’s materials module enabling users to track supplies, storage, vendors, and orders.

Researchers at the University of Catania have released miRandola, a database that provides information about extracellular microRNAs.

AB Sciex has released LibraryView, an application for identifying contaminants in food, environmental, clinical research, and forensic toxicology samples.

According to its developers, the software supports the acquisition of full scan tandem mass spectra of compounds or contaminants present in samples at high sensitivity as well as reliable compound identification using only one or two fragments. Furthermore, high-throughput labs can create their own custom libraries with retention time information, LC conditions, and associated matrices.

Dotmatics has released a new version of Vortex, the company’s data analysis and visualization tool for use in chemistry, biology, and engineering.

The release includes the OpenAstexViewer, which lets users visualize chemical structures and ligand complexes in 3D and 2D. Researchers can now explore their data using surface and contour plotting techniques, and they can aggregate data as well as spot plate irregularities using a new function. Vortex also includes a new internal webserver that allows external applications such as PyMol interact with it.

Velvet 1.2.08 is now available here.

Labtiva, a subsidiary of Macmillan Publishers’ Digital Science, has launched ReadCube Access, a pilot program that provides libraries and institutions with access to scientific articles in non-subscribed journals.

The University of Utah and Macmillan's Nature Publishing Group will be the program’s first participants, although Labtiva said it is working to add new publishers and institutions to the program.

During the pilot, expected to last until the end of the current semester, the University of Utah library will pay $5 to $10 for each article download. Researchers at the university can also choose to rent an article for 48 hours, which will cost the library $3 to $6.

When ReadCube is fully launched, exact pricing for articles and restrictions on access may change.

CummeRbund 2.0.0 is available here.

The release includes several new options, features, and bug fixes and is the first stable release version to fully support Cuffdiff2.

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

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.