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Downloads and Upgrades: NuGenesis 8, TopHat, Cufflinks, and More


Waters Corporation has released NuGenesis 8, the latest version of its workflow and documentation solution. The system provides tools to link analytical laboratory data systems and business information technology systems as well as to guide laboratory analysts through routine standard operating procedures.

The program also captures and catalogs information from disparate sources and provides access to a suite of information management tools including sharing, reuse, and sample management.

The developers of TopHat and Cufflinks have published in Nature Protocols a bioinformatics protocol for analyzing RNA-seq data.

The protocol covers read alignment with TopHat, gene and transcript discovery with Cufflinks, annotation analysis with Cuffmerge and Cuffcompare, differential expression analysis with Cuffdiff, and visualization with CummeRbund. Several variants of the protocol are included for those who wish to forgo certain analysis steps, such as gene discovery.

The developers of the Structural Classification of Proteins, or SCOP, and ASTRAL databases have released the first version of the combined resources, dubbed SCOP 1.75A, which includes bug fixes and automated classification of several new Protein Data Bank files

Both databases are now available through a single web interface.

Geschickten said this week that it has released a new solution that combines its cloud-based platform, iOMICS-Research, and its custom data analysis service called Data2Knowledge.

Molegro has released Molegro Virtual Docker 5, the most recent release of its platform for predicting protein-ligand interactions.

This release lets users take advantage of graphics processing units to speed up their docking simulations. The GPU acceleration features in Molegro Virtual Docker require a NVIDIA GeForce graphics card or NVIDIA Tesla GPU with CUDA support.

The Scan

Boosters Chasing Variants

The New York Times reports that an FDA advisory panel is to weigh updated booster vaccines for COVID-19.

Not Yet

The World Health Organization says monkeypox is not yet a global emergency, the Washington Post reports.

More Proposed for Federal Research

Science reports that US House of Representatives panels are seeking to increase federal research funding.

PLOS Papers on Breast Cancer Metastasis, Left-Sided Cardiac Defects, SARS-CoV-2 Monitoring

In PLOS this week: link between breast cancer metastasis and CLIC4, sequencing analysis of left-sided cardiac defects, and more.