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Downloads & Upgrades: Jun 25, 2010


Version 33 of the Reactome Knowledgebase is available here.

The new release includes a new topic, chromosome maintenance. Topics with new or revised information include axon guidance, synaptic transmission, transmembrane transport of small molecules, metabolism of proteins, diabetes pathways, signaling in the immune system, and signaling by GPCR.

GenBank 178.0 is available via ftp from the National Center for Biotechnology Information.

Release 178.0 comprises approximately 116 gigabases and 120 million entries from non-WGS, non-CON sequences, and 168 gigabases and 58 million entries from WGS sequences.

Uncompressed, release 178.0 flat files require roughly 444 gigabytes for sequence files only. The ASN.1 data require approximately 364 gigabytes.

Symyx Technologies has released the Symyx Direct 7.0 data cartridge, a system for registering, searching, and retrieving chemical and biological entities stored in relational databases.

Symyx Direct 7.0 supports natural post-translational modifications and custom modifications, the company said. It also includes a new, hybrid representation "that combines the best features of bioinformatics and cheminformatics notations."

SeqMonk v0.10.0, a software tool for visualizing and anaylyzing high-throughput mapped sequence data, is available here.

New features include directional quantitation probes, support for either removing duplicate reads upon import or ignoring them in every quantitation method, the ability to extend reads when importing them to facilitate the analysis of single-end ChIP-seq data, and the ability to update genome annotation sets when new annotations become available.

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.