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Ludesi 2D Interpreter, SPROUT 6.0, Taverna, expO, Cytoscape, Virtual Cell, BioPerl 1.5.0, GenomeViz

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Ludesi, a proteomics informatics developer based in Lund, Sweden, has released Ludesi 2D Interpreter, an online tool for statistical evaluation of 2D gel data, at http://www.ludesi.com. The software is freely available for academic users.


SimBioSys has released SPROUT 6.0, a de novo ligand-design package designed for parallel-processing environments.


Version 1.0 of Taverna, a workflow design and enactment environment developed as part of the myGrid project, has been released at http://taverna.sf.net. Taverna allows users to construct complex analysis workflows from components located on both remote and local machines, run these workflows on their own data, and visualize the results.


The International Genomics Consortium’s expO (Expression Project for Oncology) project has released clinically annotated gene expression profiles for 60 tumor specimens through NCBI’s Gene Expression Omnibus at http://www.ncbi.nlm.nih.gov/geo/. Over the next three years, IGC expects to obtain 2,000 to 3,000 tumor specimens representing a broad spectrum of malignancies, and 500-1,000 normal tissues.


The Cytoscape project has released version 2.0 of the ExpressionCorrelation plug-in at http://cytoscape.org/new/plugins2.php. The plug-in enables Cytoscape users to correlate genes or conditions in an expression matrix file loaded into Cytoscape. The resulting correlation network is visualized in Cytoscape and can be filtered based on a given correlation threshold.


Virtual Cell version 4 has been released at http://www.vcell.org. Enhancements in version 4 include faster model-loading and -saving and improved simulation performance; support for multiple open models with improved reaction copy-and-paste; explicit surface representation, viewing, and smoothing for 2D and 3D geometries; automated unit calculation and consistency checking; and enhanced naming support.


BioPerl 1.5.0, a developer’s release, is available for download at http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2 and http://bioperl.org/DIST/bioperl-1.5.0.zip.


The Institute of Medical Microbiology in Giessen, Germany, has released GenomeViz, a package for plotting data from microbial genomes on circular genome plots, at http://www.uniklinikum-giessen.de/genome/genomeviz/intro.html.

 

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