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Rosetta Elucidator, ClinProTools 2.1, flexImaging 2.0, WARP-LC 1.1, Insilicos Proteomics Pipeline, Proteus, LightSight, GeneSpring MS, Cytoscape 2.3 beta 1, Protein Data Bank, Rubicon, Brood 1.0, UniProt 8.0, Treefinder

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Rosetta Biosoftware has released version 2.0 of its Rosetta Elucidator protein expression data analysis system. The new release supports data from Thermo Finnigan LTQ FT and LTQ Orbitrap, Waters Q-TOF Premier, and Applied Biosystems QSTAR instruments, and integrates with the Mascot, Sequest, and Sage-N Research Sorcerer search engines. The software also includes improvements in its visualization and productivity tools, including a 2D image viewer for evaluating LC/MS data, and a tool to rapidly generate a list of differentially expressed proteins.


Bruker Daltonics has released ClinProTools 2.1 and flexImaging 2.0. The integrated software packages enable users to merge statistical analysis on MALDI-TOF profiling spectra with molecular images of tissue distributions of peptide and protein biomarkers.

ClinProTools, the company's biomarker panel analysis software, now includes additional features for data analysis and visualization, including a proprietary supervised neural network algorithm that complements the existing support vector machine and modified genetic algorithm. ClinProTools 2.1 also includes principal component analysis for unsupervised data analysis.

Bruker also released WARP-LC 1.1, a software suite for LC-MS/MS protein analysis using isotope labeling. The software supports all current industry-standard label chemistries as well as multiplexed quantification.


Insilicos has launched Insilicos Proteomics Pipeline, a software system for analyzing proteomics data. IPP is built upon the Trans-Proteomic Pipeline developed at the Institute for Systems Biology, but is able to run the software up to 20 times faster than the open source version, the company said.


GenoLogics Life Sciences Software has upgraded its Proteus software to include Automated Informatics, a technology framework for pipelining and analytics automation. The new version of the software is also integrated the ISB's Trans-Proteomic Pipeline.


Applied Biosystems has launched LightSight, a software package for metabolite identification with the 4000 Q TRAP mass spectrometer and other triple quadrupole and hybrid linear ion trap mass spectrometers from ABI/MDS Sciex.


Agilent Technologies has launched GeneSpring MS, a version of its GeneSpring analysis software for proteomics, metabolomics, and biomarker discovery. GeneSpring MS allows researchers to import, store, visualize, and analyze gas chromatography/MS and liquid chromatography/MS data.


Cytoscape 2.3 beta 1 is available for testing at http://chianti.ucsd.edu/Cyto-2_3-beta/cytoscape-v2.3_beta1.zip. The release includes several new features like fast rendering and saving session, "but because of this the release will need extra amounts of testing to insure a quality release," the developers noted. A testing guide is available at http://cytoscape.org/cgi-bin/moin.cgi/Testing_Instructions.


The Protein Data Bank has introduced a set of web services to help software developers build tools that interact more effectively with PDB data. A list of the web services, which include Blast, Fasta, PubMed, and SNP queries, is available at http://www.rcsb.org/robohelp_f/#webservices/summary.htm.


Indigo BioSystems has launched Rubicon, a suite of applications to manage scientific data. The software captures proprietary, machine-readable data at the moment of its creation and archives it in an open format, the company said.


OpenEye Scientific Software has released Brood 1.0, an application for bioisostere prediction. Brood searches databases of known chemical fragments to identify molecular fragments that are similar to a query fragment and identifies bioisosteres by finding fragments with shape, chemistry, and electrostatics that are similar to a 3D query fragment.


UniProt 8.0 is available at http://www.uniprot.org. The current release includes 3,170,612 entries, including 222,289 from UniProtKB/Swiss-Prot and 2,948,323 from UniProtKB/Trembl.


The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the latest zebrafish assembly through the UCSC Genome Browser at ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer4/ and http://hgdownload.cse.ucsc.edu/downloads.html#zebrafish. The assembly, Zv6 (UCSC version danRer4, March 2006), was produced by the Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology and the Netherlands Institute for Developmental Biology, and includes 1.6 billion base pairs in 6.653 with a sequence coverage of approximately 6.5-7x.


Treefinder, a free software package for computing phylogenetic trees from molecular sequences, is available at http://www.treefinder.de. New features include global search from multiple start trees, a start tree generator, confidence limits for all numerical results, and simplified tree calibration.

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