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Downloads and Upgrades: Dec 10, 2010

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This week, GenomeQuest announced that it has expanded its patent search content to include sequences filed at the Chinese State Intellectual Property Office.

According to the company's analysis, more than 50 percent of Chinese patents with biological sequences are not filed in patent databases outside of SIPO.

The SIPO sequences will be available through GQ-IP, the company's online patent research solution that holds information on more than 300,000 patents, including patent number, title, abstract, assignee, inventors, dates, and patent families.

GenomeQuest said that currently more than 40,000 sequences from more than 5,000 Chinese patents are indexed and searchable in GQ-IP

GQ-IP aggregates, normalizes, curates, and updates patent information across multiple databases, including the US Patent and Trademark Office and the World Intellectual Property Organization. It also provides multiple search algorithms, including Blast and GenePast, and its result browser allows users to query, filter, and group on different fields.


The National Cancer Institute Center for Biomedical Informatics and Information Technology has released version 2.0 of the caBIG Algorithm Validation Toolkit, an imaging software that provides tools to support medical image measurement validation research.

According to the CBIIT, the major enhancements for this version include an Insight Toolkit-based open source segmentation algorithm, reader variability, multiple regression analysis, factorial ANOVA analysis, improved contour editing, and an AVT2 coding scheme, among other features.

Also this week, the NCI's Cancer Biomedical Informatics Grid launched version 2.0 of the caBIG Life Sciences Domain Analysis Model.

This release includes a consistent level of abstraction and clearer model with traceability to the Biomedical Research Integrated Domain Group, or BRIDG, by direct inclusion of the relevant classes; alignment with version 3.0.2 of BRIDG; and the generic assay model, developed in collaboration with the HL7 clinical genomics working group, is included as a core component of the LS DAM.


LabKey Software has released LabKey Server 10.3.

In addition to other enhancements, version 10.3 lets users analyze sequences, quality scores, and multiplex identifiers directly or export them to FASTQ files for analysis in other tools. The new version also allows users to import high-throughput, 384-well plate and multi-plate NAb assay runs, and ensure data integrity with a read-only file repository. The tool also lets users integrate with the open source Galaxy platform and create data visualizations, and includes new genotyping tools


This week, IO Informatics released Knowledge Explorer version 3.3.

The latest version of the tool includes a new extract, transform, load, or ETL, functionality that lets users build semantic knowledge bases from multiple data sources. Users can also integrate experimental data, natural language processing results, public data sources, and clinical information


This week, the Foundation for the National Institutes of Health’s Biomarkers Consortium announced that data from a proteomics study performed utilizing plasma samples from the Alzheimer’s Disease Neuroimaging Initiative is now available for download and further analysis.

This project is the first part of a multi-phased effort seeking to utilize samples collected by ADNI to qualify multiplex panels in both plasma and cerebrospinal fluid to diagnose patients with Alzheimer’s disease and monitor disease progression.


Researchers at the University of Oslo in Norway and the Hospital for Sick Children in Toronto, Canada, have launched iRefWeb and iRefIndex to provide access to data on protein-protein interactions consolidated from major public databases.

iRefWeb, a web interface to the iRefIndex resource, lets users query and retrieve protein interaction data from source databases using a variety of query types and filters. Users may also compare side-by-side curation of interactions from the same paper by multiple databases.

iRefIndex provides an index of protein interactions available in a number of primary interaction databases such as BIND, BioGRID, CORUM, DIP, MINT, IntAct, HPRD, MINT, MPact, MPPI, and OPHID

iRefIndex data is also accessible via a Cytoscape plugin called iRefScape


Qlucore announced the release of Qlucore Omics Explorer 2.2 this week.

The latest version of the data analysis software lets users import data generated on Agilent microarrays and includes inbuilt pre-settings for well-defined data types and an interface for the normalization of other data types.

The tool is also available, for the first time, in a 64-bit version.


The Protein Data Bank has been updated.

Updated features include MyPDB storage of annotations on particular PDB entries; access to transporter classification information; new data distribution summaries for search results; access to data from the Structural Biology Knowledgebase such as protein targets, biological annotations, and clones; and high-resolution image generation.


This week, the Broad Institute released MSigDB 3.0, the latest version of its database of annotated gene sets.

Included in this release are a total of 6,796 gene sets; more than 1,200 new gene sets drawn from scientific journals; 430 new canonical pathway gene sets from the Reactome pathway database; new gene set annotations, including direct links to corresponding microarray datasets in the Gene Expression Omnibus and ArrayExpress and direct links to chemical structures in PubChem; and new options to display and download gene sets as Entrez Gene identifiers, in addition to gene names and microarray probe set identifiers.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.