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GenomeStudio, MetWorks 1.2, Nexus Copy Expression 1.0, Symyx Chemistry Extensions for KNIME, G2 ADME Model, ParallelR 1.2

Illumina plans to launch in November a new software program called GenomeStudio to support data for the new mRNA-Seq cDNA sequencing application for its Genome Analyzer platform. According to the company, the software will enable the simultaneous analysis of over 100 million sequence reads, in addition to microarray data, all within the same project workflow paradigm.
GenomeStudio will also offers application programming interfaces that enable data integration with third party software providers for more advanced downstream analysis.

Thermo Fisher Scientific has launched MetWorks 1.2, an updated version of its metabolite identification software. MetWorks is a data-mining tool for small molecules that can be used to search for and identify a variety of metabolites.
MetWorks 1.2 has a new graphical user interface with multiple mass defect filters, which display the distribution of parent and potential metabolites.
The company said that when the software is used with a Thermo LTQ Orbitrap mass spectrometer, it can facilitate the extraction of low levels of metabolite ions, even when they are three to four orders of magnitude less abundant than the background matrix ions.
This latest version of the software also features a new summary report, as well as  new analyte and modification managers that calculate accurate masses for parent compounds and potential biotransformations using standard molecular formulae.
MetWorks software is compatible with all Thermo Scientific mass spectrometers capable of performing MS/MS and MSn fragmentation. 

BioDiscovery announced the release of Nexus Copy Expression Version 1.0 for gene expression analysis with a new interface for using gene expression results to associate sample attributes with gene annotations and biological processes.
Nexus Expression is platform independent, the company said, and supports all array platforms including Affymetrix, Agilent, Illumina, Roche NimbleGen, and custom arrays.

Symyx Technologies announced the release of version 1.0 of Symyx Chemistry Extensions for KNIME.
KNIME is an open-source, extensible data exploration platform for chemists to create visual data pipelines. It was developed at the University of Konstanz, Germany, where it continues to be maintained and updated.
The company said that the Symyx Chemistry Extensions enhance KNIME's open-source pipelining software with Symyx's chemistry capabilities.
The extensions include reaction-based enumeration, stereoenumeration, specific enumeration, and Rgroup decomposition.
Symyx Chemistry Extensions for KNIME use the Symyx Cheshire 4.1.1 chemical scripting language and prototyping environment. They are distributed under the Aladdin “no charge” public license. To fully utilize the product, customers require a license for Symyx Cheshire software.

G2 Research, a Lake Tahoe, Nev.-based consulting company focused on data, models, and tools to develop pharmacokinetic models, announced the commercial availability of its ADME Model in vivo and in vitro assay data set suitable for building pharmacokinetic models.
The set contains assay data for nearly 600 compounds, including more than 9,500 individual data points, the company said, such as protein binding, CYP 2D6 and 3A4 inhibition and thermodynamic solubility at five pH values
A related set of human in vivo data corresponding to the compounds used in the in vitro assays is also available. Analysis of these data have led to target in vivo profiles for the development of ADME models.
A comprehensive exclusive in vivo rat ADME data set is available as well, the company said.
Based on original research conducted by NaviCyte, acquired by Trega Biosciences in 1998, and subsequently by Lion Bioscience in 2001, the data sets consist of individual in vitro and in vivo assay data points of hundreds of hand-selected pharmaceutical compounds. 
The compounds represented in the data sets were chosen to produce robust, diverse data pools of in vitro and human pharmacokinetic clinical data, consisting of both drug development successes and failures, to train ADME models.
The data is provided in Oracle, Excel, or flat text file format.

New Haven, Conn.-based software provider Revolution Computing has launched ParallelR version 1.2.
ParallelR lets R users complete statistical analyses “much more quickly” by taking full advantage of multiprocessor systems and network systems, according to the company.
Computations can be run across heterogeneous hardware configurations, including 32 bit, 64 bit, SMP, and cross-platform configurations, such as combinations of Linux, Windows, and Mac OS X operating systems.

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