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Downloads and Upgrades: Dec 24, 2010

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Version 35 of the Reactome Knowledgebase is available here.

The release includes a new topic, circadian clock. Topics that contain new, revised and updated information include the immune system signaling module, interactions of the DSCAM immunoglobulin superfamily proteins, GABA receptor activation in synaptic transmission, regulation of mRNA stability by AU-rich elements, vitamin B1 metabolism and molybdenum cofactors biosynthesis, vitamin A uptake in enterocytes, transport of glycoproteins to the golgi, and additional transport systems.

The developers also announced that the Reactome functional interaction plugin is available from Cytoscape. The plugin provides users with access to the Reactome functional interaction network, a set of protein-protein interaction pairs scored by quality that links proteins curated in Reactome to other human proteins and covers close to 50 percent of human proteins. This plugin is useful in the discovery of network patterns related to cancer and other types of disease, the developers said.


Velvet 1.0.16 is available here.

In this release, the developers corrected errors in the longsequences option, enabled users to tune the percentage of paired-end reads with respect to the expected value, and included a set of options that help users avoid copying sequence files uselessly, among other features.


University of California, San Francisco's Resource for Biocomputing, Visualization, and Informatics and SRI's Pathway Tools have released the BioCyc Plugin for Cytoscape.

According to the developers, the plugin allows users to search pathway repositories supporting Pathway Tools version 14.5 or better, and load those pathways into Cytoscape in the BioPAX format.

In addition, RBVI and its collaborators at the Gladstone Institutes have also released the nodeCharts plugin.

The plugin provides a CyCommand interface for drawing pie, line, and bar charts onto nodes using either attribute data or arbitrary data values provided as part of the command.

Additional details about the plugin are available here.


GenBank 181.0 is available via FTP from the National Center for Biotechnology Information.

Uncompressed, version 181.0 flatfiles require roughly 468 gigabytes for sequence files only or 503 gigabytes to include the short directory, index, and text files. The ASN.1 data require approximately 384 gigabytes.


Researchers at the Wistar Institute have released the Mammalian Promoter Database, an online tool that helps users locate and identify gene promoters.

According to the developers, MPromDb integrates the genome sequencing data generated at Wistar with publicly available data on human and mouse genomics from resources like the Gene Expression Omnibus and the Encyclopedia of DNA Elements and includes several complete genome sequences and assembled sequences from the 1000 Genomes Project.


Thomson Reuters and ChemAxon have partnered to provide Thomson's Markush Structures database and patent data to users of ChemAxon’s JChem chemical software platform.

The Markush Structures database contains data on the relationship or “families” of 550,000 patents and 1.7 million related, exemplified, specific compounds. ChemAxon’s JChem software lets users structure and visualize chemical compounds for property prediction, virtual synthesis, screening, and drug design.


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.