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Downloads & Upgrades: Ingenuity iReport; BioJava; NPG's Linked Data Platform

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Ingenuity has optimized its Ingenuity iReport to support Life Technologies' TaqMan gene expression assays.

Ingenuity said that lReport has been optimized for several TaqMan gene expression assay formats, including TaqMan Array Card and OpenArray file types. The combined resource is expected to provide a faster and more comprehensive understanding of pathways, processes, and diseases relevant to gene expression results, the company said.


BioJava 3.0.3 is available here.

The release includes improvements to the web service module; support for SIFTS-PDB to UniProt mapping; and improved support for working with external protein domain definitions among other features.

BioJava Legacy 1.8.2 is also available.

The release incorporates several new features, including streaming and low-level parsers for the FASTQ package and bug fixes.

BioJava Legacy is a continuation of the version 1.x releases of BioJava.


Nature Publishing Group is providing access to its publication data via a semantic web system dubbed NPG's Linked Data platform.

The platform includes more than 20 million resource description framework statements, including primary metadata for more than 450,000 articles published by NPG. The datasets include basic citation information — such as title, author, and publication date — as well as NPG-specific ontologies.

It lets users query, explore, and extract data and relationships about articles, contributors, publications, and subjects. Users can run web-standard SPARQL Protocol and RDF Query Language queries to obtain and manipulate data stored as RDF. The platform also uses standard vocabularies such as Dublin Core, FOAF, PRISM, BIBO, and OWL; and its data is integrated with existing public datasets such as CrossRef and PubMed.


The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.