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IMG/M, structureViz, UCSC Genome Browser, MiMI index, flexImaging 2.0, MGLTools Suite, Cardiovascular PhysioLab, SynaMer, jelMarker, CNSsolve, TMA Foresight

The US Department of Energy’s Joint Genome Institute has released an upgrade of its IMG/M (Integrated Microbial Genomes with Microbiome Samples) data-management system for metagenomics data. IMG/M includes tools for analyzing metagenomic data for microbial communities in the context of reference isolate genomes. The update includes aggregate genome data from recently published studies, such as biological phosphorus-removing sludge, human distal gut, a gutless marine worm, and obese and lean mouse gut. IMG/M also includes three simulated metagenome data sets used to benchmark assembly, gene prediction, and binning methods. IMG/M is available here.

The University of California, Santa Cruz, Resource for Biocomputing, Visualization, and Informatics has released structureViz, a Cytoscape plug-in that integrates Cytoscape’s network visualization capabilities with UCSF’s Chimera software for visualizing macromolecular structures. The structureViz plug-in provides commands to open structures in UCSF Chimera, align open structures using Chimera's Sequence/Structure tools, close structures that are currently open, and exit Chimera.

The Genome Bioinformatics Group at the University of California, Santa Cruz, has made the March 2006 release of the cat (Felis catus) genome available through the UCSC Genome Browser. The assembly was produced by the Broad Institute of MIT/Harvard and Agencourt Bioscience. The genome has been sequenced to 2X coverage and has a total contig length of around 1.6 Gb spanning around 4.0 Gb. The sequence and annotation data are available through the FTP server here or the downloads page here.

The University of Michigan has released the Michigan Molecular Interactions (MiMI) index, a database that integrates information from multiple protein interaction repositories, including BIND, HPRD, and others. The developers have created a “provenance model” that tracks where each piece of data came from, and what processes have been performed upon it. The current version includes 119,880 molecules, 330,152 interactions, and 579 complexes.

Bruker Daltonics has released flexImaging 2.0, a new version of its software for acquiring and evaluating MALDI-TOF and TOF/TOF imaging data. The software enables color-coded visualization of the distribution of biomarkers or absorbed drugs and their major metabolites. The new version provides "class imaging" as an extension to the previously available "mass imaging.” According to Bruker, class imaging is a proprietary method for classifying tissue types and determining the class membership of comparable tissues or biopsies from other individuals or from animals used in drug development.

The Scripps Research Institute has released version 1.4.4 of its MGLTools Suite, which includes Python Molecular Viewer, AutoDockTools, and the VISION visual programming environment.

Entelos has completed its Cardiovascular PhysioLab platform, a large-scale simulation of cholesterol regulation, atherogenesis, and cardiovascular risk. The company said it is already conducting research partnerships with three undisclosed pharmaceutical customers using the platform. The Cardiovascular PhysioLab platform includes four submodels: cholesterol metabolism; atherogenesis; plaque stability; and cardiovascular risk.

Synamatix has released SynaMer, software for processing sequence reads for large-scale genome assembly. The software, developed in collaboration with an undisclosed genome research institute, was recently used to process 23 billion base pairs of sequence data from the macaque genome in 3.5 hours, producing as output all overlapping 96-mers from the assembly reads, the company said.

SoftGenetics has released jelMarker, a software tool for converting slab gel TIFF, BIP, JPEG, and TXT files into a standard format for importing electrophoresis data into its GeneMarker software. The company said that it developed jelMarker “in response to the growing demand for software that can analyze fluorescence, chemiluminescence and autoradiography gel image files.”

YaleUniversity has released version 1.2 of CNSsolve (Crystallography & NMR System) here. The software offers a multi-level hierarchical approach for commonly used algorithms in macromolecular structure determination, including heavy atom searching, experimental phasing, density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation.

Premier Biosoft International has launched TMA Foresight, a statistical tool for tissue microarray data analysis. TMA Foresight includes mean, sum, and variance statistics, as well as more advanced data correlation such as hierarchical clustering, Kaplan Meier plots, and Cox’s proportional hazard analysis.

Filed under

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