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Molecular Operating Environment, BioRS Integration and Retrieval System, The Cancer Genome Atlas, The PerfectCircle, SHARe, Bioinformatics Toolbox 3.0

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Chemical Computing Group has released the 2007.09 version of the Molecular Operating Environment. The release contains new technology for scaffold replacement methodology integrated with pharmacophore discovery tools; Protonate3D for assignment of ionization and proton geometry in macromolecules; pipeline tools for tautomer and ionization state enumeration of small molecules; and LigX, an application for structure-based ligand optimization.
 
Chemical Computing Group's software platform integrates visualization, simulation and methodology development in one package. MOE contains a wide variety of built-in applications in the fields of cheminformatics, bioinformatics, computer-aided molecular design and molecular modeling, and runs on Windows, Linux, Macintosh or Unix.
 

 
Biomax has released a new module for the BioRS Integration and Retrieval System, an application providing simultaneous searches in multiple biological and biomedical databases.
 
The new module provides standard sequence similarity search and multiple alignment tools for querying nucleotide and protein sequences. With this module, the BioRS form allows text fields to be searched while simultaneously using BLAST similarity and pattern searches with a sequence field.
 
The integrated text and similarity search allows fast and specific results focusing on a topical area, the company said. Search results provide access to sequences in different formats as well as pair-wise and multiple sequence alignments.
 

 
The National Cancer Institute and the National Human Genome Research Institute have released the initial version of The Cancer Genome Atlas data portal. The portal is a storage and data management tool for TCGA data.
 
To help create a fully integrated version of the portal in the coming months, NCI and NHGRI are seeking input and feedback on the Data Portal can be accessed at http://cancergenome.nih.gov/dataportal.
 
The Data Portal includes the first of many sets of data from TCGA, and will be continually updated as data are generated, NCI and NHGRI said.
 
The Cancer Genome Atlas is a three-year pilot project designed to accelerate understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.
 

 
Bar Harbor Technology has launched The PerfectCircle, a suite of products comprised of GeneSieve Bioinformatics, StellARray Real-Time PCR arrays, and Global Pattern Recognition Bioanalysis applications. Together they allow scientists to perform gene expression research in an innovative way, the company said.
 
The company recently announced the completion of a Series A round of financing as well as a development award from the Maine Technology Institute for $334,632 towards development of “human genetic profiling products.”
 

 
The National Institutes of Health has launched an extensive collection of genetic and clinical data and offered it freely to researchers worldwide. Called SHARe (SNP Health Association Resource), the web-based dataset enables researchers to access data from large population-based studies, starting with the Framingham Heart Study. Funded by the NIH's National Heart, Lung, and Blood Institute, SHARe will accelerate discoveries linking genes and health, thereby advancing scientists' understanding of the causes and prevention of cardiovascular disease and other disorders.
 
SHARe is accessed through dbGaP, or the database of Genotypes and Phenotypes and is available here.
 

 
The MathWorks has launched an updated version of its Bioinformatics Toolbox for Matlab, which supports computational biologists and research scientists in their efforts to effectively prototype new algorithms and build applications for drug research, genetic engineering, and other genomics and proteomics projects.
 
Among the new features of Bioinformatics Toolbox 3.0 are new capabilities to improve analysis and visualization of microarray and mass spectrometry data.
 
Enhancements to Bioinfomatics Toolbox allow users to normalize and clean microarray data, calculate gene expression, and perform circular binary segmentation and false discovery rate estimation. Toolbox 3.0 includes visualization capabilities that enable users to plot chromosome ideograms, too.

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