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Downloads and Upgrades: Oct 8, 2010


The 18th release of the BioModels Database is available here

This release contains 157 new models. According to the developers, there are now 269 models in the curated database and 361 models in the non-curated database, comprising a total of 79,224 species and 109,091 reactions. The database now features 20,426 cross-references.

The release also includes updated versions of XPP and BioPAX Level 2 converters and two new ones, BioPAX Level 3 and Octave.

Complete Genomics has expanded its suite of Complete Genomics Analysis Tools to help its customers interpret and compare data and results from multiple genomes. According to the company, this could enable them to find potential somatic mutations in a tumor-normal comparison as part of a cancer study, for example.

The updated suite includes a custom annotation tool, which allows users to merge variant files with files containing user-specified annotations. This enables researchers to filter the data to focus on the regions that are most important for a given study or sample.

Version 34 of the Reactome Knowledgebase is available here.

Version 34 includes a new topic, interactions of the immunoglobulin superfamily member proteins covering nephrin and signal regulatory protein family interactions. Topics that contain new or revised and updated information in this release include transmembrane transport of small molecules, metabolism of proteins, hemostasis, signaling in the immune system, signaling by insulin receptor, signaling by GPCR, integration of energy metabolism, and synaptic transmission.

Glencoe Software, the Journal of Cell Biology, and Rockefeller University Press have released a new version of the JCB DataViewer, which supports new image data formats and provides new functionality for its users.

The latest release lets JCB readers download image data in the OME-TIFF format, the open scientific image data format released by the Open Microscopy Environment that stores image metadata — information about the original imaging system and data acquisition parameters. This allows readers to access how the data included in a published paper were originally acquired and to re-analyze the data using their own software.

The University of California, Santa Cruz, Bioinformatics Group has updated the UCSC Genome Browser to include the latest release of the software and a change in the way the tracks image is drawn.

This week, GeneGo announced that it has integrated GenomeQuest's Sequence Data Management platform with its MetaCore and MetaDrug software.

Researchers can now use GenomeQuest's platform to identify genes of interest in their data and then pass that gene list along with their associated expression values to the GeneGo suite of pathway analysis software tools. The combined tools "will lead users from raw sequence runs to functional hypothesis generation of drug targets and biomarkers" and "leverage disease pathology maps developed in MetaMiner programs in oncology, CNS, metabolic, respiratory diseases and other therapeutic areas," the company said.

The Protein Data Bank website has been updated to include improved navigation of the Molecule of the Month archive, a PDBMobile application for the iPhone, new ways to explore search results using data distribution summaries, integration with binding affinity data from BindingDB, and new help features including a sitemap and glossary.

Additional details are available here.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.