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DomainGraph 1.0, Pathway Studio 6, BioXM 3.0, PharmGKB, GenBank 167.0, Prous Science Integrity Predictive Pharmacology Module, PSILO

The Max Planck Institute for Informatics has launched DomainGraph 1.0, a Cytoscape plug-in. DomainGraph takes a protein interaction network as input and computes and displays the underlying domain-domain interactions. Additionally, it supports the integration of exon expression data measured using the Affymetrix Human Exon 1.0 ST Array.
DomainGraph 1.0 has been tested to work with Cytoscape 2.5 and 2.6 and is available here.

Ariadne Genomics has launched Pathway Studio 6, which features gene expression analysis tools, updated pathway collection, and a new interface.
It organizes and visualizes knowledge from many data sources to help researchers discover and analyze pathways affected in an experiment, or build regulation networks from the most differentially expressed genes using the ResNet 6 database, which includes 1.5 million relationships extracted from 17,000 million PubMed abstracts and 61 full text journals.

Biomax Informatics has released an upgrade of its BioXM knowledge management environment, which integrates information from different data sources to dynamically build semantic networks, which can then be mined and analyzed.
BioXM 3.0 now introduces a set of tools specifically developed for scientific interpretation of semantic networks, such as biological pathways or biomedical relationship graphs, the company said.
The new version of the software also includes a “high-performance” analysis API for integrating tools such as R and BioConductor scripts or other third-party applications.

Version of the Pharmacogenetics & Pharmacogenomics Knowledgebase, or PharmGKB, is available here.
The new release includes automatically mined associations between genes, variants, drugs, and phenotypes based on the Pharmspresso system, which is a modification of Cal Tech’s Textpresso.  
These associations are separated from the human-curated ones, which are also available. The new release also includes a new grading system for information: one star for automated inferences, two stars for "minimally curated" data, and three stars for full curation. PharmGKB also offers access to much of its data via a web services interface.

GenBank Release 167.0 is now available via FTP from the National Center for Biotechnology Information here.  
Uncompressed, the Release 167.0 flat files require roughly 357 GB for sequence files only or 381 GB, including the “short directory,” “index,” and *.txt files. The ASN.1 data require approximately 326 GB.
Release 167 includes 95,033,791,652 base pairs and 92,748,599 entries of non-whole-genome shotgun data. For WGS sequences alone, release 167 has 118,593,509,342 base pairs and 40,214,247 entries.
GenBank “index” files are now provided without any EST content, and without most GSS content, NCBI said.

Thomson Reuters has launched Prous Science Integrity Predictive Pharmacology Module, a tool that is part of the Prous Science Integrity platform, to probe the mechanisms of action of thousands of bioactive compounds.
The Predictive Pharmacology Module was developed at the Prous Institute for Biomedical Research. It details up to three potential mechanisms of action for nearly 100,000 lead compounds with chemical structures in Prous Science Integrity and includesvisualization tools.

Chemical Computing Group has released PSILO, or Protein Silo, a database system that provides a consolidated repository for proprietary and non-proprietary macromolecular and protein-ligand structural information.
PSILO centralizes structural data, whether proprietary or public, and makes them searchable using a web browser. It also allows users to store comments or report perceived problems with deposited structures and the authors of the structures are automatically notified and can respond or deposit a corrected version of a structure.

Filed under

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.