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Thermo Finnigan, EMBL Nucleotide Sequence Database, Theoretical Biophysics Group, Istituto di Chimica Farmaceutica e Tossicologica, Ensembl

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Thermo Finnigan, a Thermo Electron subsidiary, has launched version 2.0 of its Metabolite ID software for metabolic LC/MS/MS analysis. The new version includes an isotopic search algorithm that enables users to identify patterns and peaks of parent drugs and modifications and search custom isotope patterns for isotopically labeled drug modifications.

Release 73 of the EMBL Nucleotide Sequence Database is available from ftp://ftp.ebi.ac.uk/pub/databases/ embl/ release/ (UK), ftp://bio-mirror.net/ biomirror/embl/release/ (US), and other mirror sites. Release 73 is about 14.5 GB compressed and 91 GB uncompressed and contains 20,857,746 sequences comprising 27,903,283,528 nucleotides, an increase of about 20 percent over release 72 in September.

The Theoretical Biophysics Group at the University of Illinois has released updates for its BioCore web-based biological collaborative research environment (www.ks.uiuc. edu/Research/BioCoRE). New features include supercomputer job management, shared molecular visualization, and a web-based graphical form that researchers can use to create input files for the NAMD molecular dynamics simulation program.

BioPython 1.10 is now available at: www.biopython.org/Download/. It requires Python version 2.2. New features include a registry framework for generic access to databases and parsers, several new algorithms and parsers, and a number of bug fixes.

Release 4.1 of W2H, a web interface for EMBOSS and GCG, is available from the German Cancer Research Center at ftp://genome.dkfz-heidelberg.de/pub/w2h.

VEGA 1.4.3, a program to convert, manage, and visualize 3D structures, is available from Milan’s Istituto di Chimica Farmaceutica e Tossicologica at www.ddl.unimi.it/. New features include an MDL Molfile saver and multi-model PDB support for trajectory analysis.

A preliminary rat Ensembl website (www.ensembl.org/Rattus_norvegicus/) is now available. The site does not yet display predicted genes. The completed website is scheduled for release in February 2003.

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