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Downloads and Upgrades: Pacific Biosciences, Discovery Studio 3.5, and more.


This week, Pacific Biosciences released a software tool for its single-molecule, real-time sequencer that detects DNA base modifications associated with epigenetic regulation and DNA damage during the sequencing process.

According to the company, the new analysis tool enables users to detect and visualize these modifications. It works by measuring the rate of DNA base incorporation during the sequencing process. Researchers can also use the tool to re-analyze existing data to detect methylation and other base modifications.

Accelrys has released Discovery Studio 3.5, the latest version of its modeling and simulation software for small- and large-molecule life sciences research and development.

The release includes a validated ligand-profiling database for drug repurposing studies; tools to assess the development potential of putative biologics; updated scientific collections which enable organizations to build, deploy, analyze, and report on complex scientific data types using Accelrys Enterprise platform; and other new features.

Velvet 1.2.07 is now available.

This release includes a new file format option, an updated version of MetaVelvet, and several bug fixes.

The National Center for Biotechnology Information has released GenBank 190.0 via ftp.

Uncompressed 190.0 flatfiles require roughly 553 gigabytes for sequence files only; or 595 gigabytes to include the short directory, index, and text files. The ASN.1 data requires approximately 454 gigabytes.

This week, the genome browser team at the University of California, Santa Cruz released new browsers for the Western painted turtle and the lesser hedgehog tenrec, as well as updated assemblies for the cow, rat, and chicken.

Definiens, a provider of image analysis and data mining solutions for quantitative digital pathology, has released version 2 of its Image Miner software.

The new release provides researchers with the ability to investigate trends and patterns in large data sets as well as view analysis details in single images. It also links readouts and underlying images; supports predictive modeling by correlating image analysis results with data from sources like patient outcome data; and provides interactive plots and data tables for real-time feedback on study trends, among other features.