The Cancer Genomics Group at the Whitehead Institute/MIT Center for Genome Research has released GeneCluster 2.0, an expanded version of their microarray analysis software. The new version can be used with proteomic and other biological data in addition to gene expression data, and adds options for pre-processing, marker selection, supervised classification, multiclass prediction, permutation test methods, and visualization. These include a gene marker selector based on neighborhood analysis, permutation tests, and visualization. The visualization feature allows users to view, sort, and color-code data by keyword. With the supervised classification feature, users can build models using weighted voting and k-nearest neighbor algorithms, as well as training models, and evaluate their performance using a test set or a variety of cross-validation options. A beta version of GeneCluster 2 is available at http://www-genome.wi. mit.edu/cancer/software/software.html.
Silicon Genetics has released MetaMine1.0, a component of its gene expression enterprise software system that examines large gene expression data repositories, and builds and distributes reports to researchers that highlight potentially valuable information, the company said. MetaMine is designed to work seamlessly with GeNet and GeneSpring, the data repository and data analysis components of Silicon Genetics’ platform.
Sunergia Group of northern Virginia has teamed up with GeneFocus of Waterloo, Ontario, Canada to introduce its third-generation genetic microarray scanners and analysis software to the US Market. The scanners include the DNAscope LM, IV & V and the Open Frame DNAscope. The DNAscopes image the entire area of a microscope slide with 5 micron pixels and high sensitivity, the company said. The Open Frame Research DNAscope is capable of reading non-standard microarrays and liquid biochips. All include MACROview microarray analysis software, which has automated spot and grid detection, automated grid alignment, spot integration and local background subtraction.