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Downloads and Upgrades: Oct 14, 2011


The Bio-Soft team at the University of Chicago has released RaptorX, a protein structure modeling web server.

According to the developers, the tool is good at modeling protein sequences that lack close homologs in the Protein Data Bank.

The genome browser team at the University of California, Santa Cruz, has released an updated browser for Saccharomyces cerevisiae.

The updated browser includes several new chromosomes for yeast from the Saccharomyces Genome Database project.

This week, Elsevier launched the Protein Interaction Browser, a new application available on its SciVerse platform that allows readers to explore protein-protein interaction networks for proteins in scientific papers.

This week, Agilent released version 2.0 of its CytoGenomics software.

The latest version of the tool supports comparative genomic hybridization and SNP-based analysis of genetically complex samples such as hematological cancer samples.

Definiens has released an updated version of its Quantitative Digital Pathology Portfolio.

The release offers updated versions of Definiens Tissue Studio and Definiens Developer XD, and adds a new component called Definiens Image Miner that integrates data mining with image analysis for biomarker-based research.

Real Time Genomics has released RTG Investigator version 2.3.

The software supports data from multiple sequence platforms, provides error-tolerant read mapping and alignment, and offers Bayesian SNP/indel variant calling among other capabilities.

A beta version of BASE 3.0 is available for download here.

The beta contains new functionality needed to support sequencing experiments with expression-like data, but may require bug fixes, according to its developers.

This week, OpGen launched Genome-Builder, a software module that provides capabilities for precision sequence assembly.

According to the developers, the tool provides a high-resolution, ordered visual map of genomic architecture that enables the detection of structural rearrangements at 10 times the resolution of traditional cytogenetic techniques.

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.