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


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 embl/ release/ (UK), 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: 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

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 New features include an MDL Molfile saver and multi-model PDB support for trajectory analysis.

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

Filed under

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.