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Sybyl 7.0, UCSC Table Browser, Map Viewer, Ensembl, International Protein Index, Tab2MAGE 1.0, MIT Press

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Tripos has released Sybyl 7.0. The latest version of the company’s molecular modeling software includes a Linux operating system upgrade to Red Hat Enterprise 3.0, expanded “borrowable” licensing capabilities for laptop computers, and expanded online technical support capabilities.


The University of California Santa Cruz Genome Bioinformatics Group has released an enhanced version of the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables. New features include a new user interface, support for generating filters that include fields from multiple tables, an enhanced schema-viewing utility, the ability to restrict queries to include only data from ENCODE regions, and an option to save large output results sets directly to a file rather than displaying them in the Table Browser.


The preliminary assembly for the Bos taurus (cow) genome, based on 3.3-fold coverage, is available through the National Center for Biotechnology Information’s Map Viewer (http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9913) and Ensembl (http://pre.ensembl.org/Bos_taurus/). Downloads of the raw contigs are also available from the Human Genome Sequencing Center at Baylor College of Medicine, which led the international cow sequencing effort (http://www.hgsc.bcm.tmc.edu/projects/bovine/). Researchers are continuing sequencing and plan to have a 6-fold draft of the bovine genome completed sometime in the first half of 2005.


The European Bioinformatics Institute has released an updated version of the International Protein Index database at ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/. The database, compiled from Swiss-Prot, Trembl, RefSeq, and Ensembl, contains 47,274 entries for human, 41,916 for mouse, and 33,308 for rat.


EBI’s ArrayExpress team has released Tab2MAGE 1.0, a spreadsheet-parsing and MAGE-ML generation tool, at http://tab2mage.sourceforge.net/. Tab2MAGE currently includes two tools, the tab2mage.pl script, and a file-checking script, expt_check.pl. With these scripts, users can perform an initial data file validation against an array design, and then generate MAGE-ML using these data files alongside a separate spreadsheet providing MIAME-compliant sample annotation.


Ensembl release 25 is now available at http://www.ensembl.org. There are no new assemblies in the release.


The MIT Press has published An Introduction to Bioinformatics Algorithms by Neil Jones and Pavel Pevzner, a book that introduces the algorithmic principles driving advances in bioinformatics. Further information on the book is available at http://www.mitpress.mit.edu/0262101068.

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