Downloads & Upgrades
SimBioSys has released eHiTS 6.1. The new version of the docking program includes a new unique scoring function for improved accuracy and offers faster docking times and improved ease of use. The company has also released a free version of its CheVi molecular visualization program. CheVi and a free evaluation version of eHiTS are available at http://www.simbiosys.ca/products/demo_request.html.
EMBOSS 4.0 is available at ftp://emboss.open-bio.org/pub/EMBOSS/. The new release includes support for the new EMBL database format, two new sequence database access methods (WsDbFetch and MRS), improved support for reading data over HTTP, enhanced help output, new applications, and updated versions of the EMBASSY packages.
Biopython 1.42 is available at http://biopython.org/. The release includes a new Genbank parser, updates to Bio.Nexus and Bio.Geo, and an object-oriented version of Bio.Cluster.
Affymetrix has released new specifications for its GeneChip-Compatible Applications Program. The new specification, available at http://www.affymetrix.com/products/software/compatible/compatible_specs.pdf, replaces the specification released in October 2005. Affy has also released Fusion SDK 1.07 through the Affymetrix Developer Network at http://www.affymetrix.com/support/developer/fusion/index.affx.
The National Center for Biotechnology Information has released RefSeq 18 at ftp://ftp.ncbi.nih.gov/refseq/release/. The release includes 2,762,164 proteins and sequences from 3,695 different organisms.
The University of Pennsylvania and the Children's Hospital of Philadelphia have released FABLE v1.0, a software package that performs document retrieval of Medline abstracts for queries of genes, transcripts, and proteins via automated text annotation. FABLE combines a named entity recognition extractor and a human gene normalizer that have been applied to all Medline records and is available at http://fable.chop.edu.
The Computational Biology Research Group at the University of Washington has released Bioverse 2.0 at http://bioverse.compbio.washington.edu/. Bioverse is a web interface for exploring the relationships among molecular, genomic, proteomic, systems, and organismal entities. Bioverse includes information on almost 500,000 proteins across 54 organisms. Each molecule is described in terms of its sequence, structure, and functions, as well its relationships to other molecules in terms of interactions and similarity.
Nucleic Acids Research has published its annual web server issue, which includes 150 papers describing web-based computational tools for analyzing DNA, RNA, and protein sequences and structures. The issue is freely available to subscribers and non-subscribers at http://nar.oxfordjournals.org/content/vol34/suppl_2/index.dtl?etoc. A complete listing of the 2005 NAR servers is available at http://bioinformatics.ubc.ca/resources/links_directory/narweb2006/.
People in the News
Ming Li, a professor in the David R. Cheriton School of Computer Science at the University of Waterloo, Ontario, has been elected a fellow of the Royal Society of Canada. In a statement, the Society described Li as an "influential international leader in the development of bioinformatics algorithms and software." Li is a co-developer of the PatternHunter homology search algorithm.