The University of California, Santa Cruz, Bioinformatics Group has released the ENCODE Integrated Regulation super-track, a collection of regulatory tracks for the UCSC Genome Browser that contain information about the mechanisms that turn genes on and off at the transcription level, from the from the Encyclopedia of DNA Elements project.
Individual tracks within the set show enrichment of histone modifications suggestive of enhancer and promoter activity, DNAse clusters indicating open chromatin, regions of transcription factor binding, and transcription levels.
The group has also developed new visualization methods that cluster and overlay the data, and then display the resulting tracks on a single screen.
A detailed description of the datasets in this track is available here.
The UCSC group has also added new functionality to the browser that lets users rearrange the order of tracks within the browser image.
GenomeQuest and SGI have collaborated on hardware and software infrastructure based on the company’s GQ-Engine to provide whole-genome analysis services for pharmaceutical companies, core labs, biotechs, government agencies, and clinics.
The services are available through GenomeQuest's data center or can be deployed directly into a customer data center.
GenomeQuest said that the WGA services will allow researchers to store, manage, and compare their sequences and annotations; assemble and align sequences from multiple instruments; use standard workflows, including variant detection, RNA-seq, and ChIP-seq; build and query enterprise-wide variant archives; and integrate with other tools and systems through an all-level API, among other features.
Simulations Plus has released GastroPlus 7.0, the newest version of its software that simulates drug absorption, pharmacokinetics, and pharmacodynamics.
Among other features, version 7.0 simulates drug-drug interaction, and creates models for predicting drug administration through ocular or pulmonary routes.
The National Center for Biotechnology Information has released Blast 2.2.24.
The new release fixes several bugs and includes new features for the Blast+ applications, such as a Blast Archive format to permit reformatting of standalone Blast searches with the blast_formatter and additional support for translated subject soft masking in the Blast databases.
Accelrys has released Symyx Notebook 6.5.
Version 6.5 features rapid material property look-up and insertion using the company’s Available Chemicals Directory sourcing database and the DiscoveryGate ChemSeek properties database. The tool also include new units that enable rapid calculations supporting the planning, recording, and scaling of synthetic routes, and a single portal for accessing and re-using captured experimental procedures and data from most legacy Symyx notebooks
Gemini II, software for mining gene expression data, is available here.
According to its developers, the software is an association-based classifier that uses an algorithm to derive rules from high-dimensional gene expression data and then uses a visualization tool for rules comparison.
EMD Millipore, the life science division of German-based Merck KGaA, has launched the Data Analysis and Report Tool, which lets drug researchers visualize G-protein coupled receptors and kinase activity.
The tool, which can be accessed through the company’s Drug Discovery Portal, projects each compound's activity profile onto a map depicting clusters of target protein families. This map provides scientists with immediate graphical insight into cross-target interactions to help drive structure-activity relationship studies.