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PLIER, Silicon Graphics Prism, BIOcrawler, ProtoNet, UCSC Proteome Browser, MosaiquesVisuOnline, Reactome

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Affymetrix has released PLIER (Probe Logarithmic Error Intensity Estimate), a method that produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error. The software is available under the GNU General Public License at http://affymetrix.com/support/developer/plier_sdk/index.affx.


SGI has released Silicon Graphics Prism, a visualization system built upon Intel Itanium 2 processors and the Linux operating environment with SGI’s graphics technology. The company said that the system is able to address terabyte-sized, highly complex data as a single image, and has a number of applications in drug discovery and biological research.


The National Cancer Institute’s Center for Bioinformatics has released an upgraded version of BIOcrawler at http://ncicb.nci.nih.gov/download. The software is a general-purpose data-querying and -browsing application that provides a keyword search interface to the NCICB caCORE systems.


Hebrew University has released version 4.0 of ProtoNet, an automated classification system for protein sequences based on hierarchical clustering, at http://www.protonet.cs.huji.ac.il/site_map.php. The new version classifies all the proteins in Swiss-Prot, supports Trembl entries, and allows users to add their own new proteins to see how they fit into the classification.


The University of California Santa Cruz Genome Bioinformatics Group has released version 1.1 of the UCSC Proteome Browser at http://genome.ucsc.edu/cgi-bin/pbGateway. The updated version includes direct access to a Proteome Browser gateway via the “Proteome Browser” menu link on the Genome Browser home page, and extended protein coverage that includes all proteins in the Swiss-Prot/Trembl databases, rather than just the human, mouse, and rat protein sets included in the previous version.


Biomosaiques Software, a bioinformatics subsidiary of Mosaiques Diagnostics and Therapeutics, has released MosaiquesVisuOnline, an online software platform for analysis of mass spectrometry data. The software is available at http://www.proteomiques.com and analyzes time-of flight-MS spectra to yield a list of analytes.


The Reactome database of biological pathways now offers export of human reactions in Systems Biology Markup Language Level 2 format at http://www.reactome.org/download/index.html.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.