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caTissue, GenBank 153.0, UCSC Genome Browser, CluSTr, Ensembl 38, Biological Crystallization Resource, wEMBOSS 1.6.0, wrappers4EMBOSS 1.4.0, Arthur Holden, David Brailer, Rick Stevens, Al Sattelberger, Kevin White

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The National Cancer Institute Center for Bioinformatics has released the caTissue Clinical Annotation Engine, a component of the caTissue suite that enables manual annotation of biospecimens with anatomic pathology data based on the College of American Pathologists checklists. The application was developed within NCI's caBIG program by a team at the University of Pittsburgh and is available at http://gforge.nci.nih.gov/frs/?group_id=20.


The National Center for Biotechnology Information has released GenBank 153.0 at ftp://ftp.ncbi.nih.gov/. The release contains 61,582,143,971 base pairs and 56,620,500 entries. Uncompressed, the 153.0 flat files require about 215 GB for the sequence files only. The ASN.1 version requires around 189 GB.


The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the latest human genome reference sequence assembly (NCBI Build 36.1, March 2006) as database hg18 in the UCSC Genome Browser. This sequence was produced by the International Human Genome Sequencing Consortium and contains four alternate haplotype regions. Bulk downloads of the data are available from the UCSC downloads server at ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/ or http://hgdownload.cse.ucsc.edu/downloads.html#human.


The European Bioinformatics Institute has released an updated version of the CluSTr database, an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. CluSTr now includes 4.8 million protein sequences -- up from 700,000 in the previous version -- as well as 6.4 million clusters for 312 organisms.

EBI has also released Ensembl 38 at http://www.ensembl.org. The release includes a new human genebuild based on the NCBI 36 assembly and including manual annotation from the Havana project. Ensembl 38 also includes a new mouse genebuild based on the NCBIm35 assembly, an updated Xenopus genebuild based on the JGI 4.1 assembly, and new navigation features.


The Biological Crystallization Resource, a database of crystallization conditions for biological macromolecules, is available from the University of British Columbia at http://www.growacrystal.com. The BCR allows users to execute multiple parameter searches to determine the optimal crystallization conditions for a macromolecule under investigation.


wEMBOSS 1.6.0 and wrappers4EMBOSS 1.4.0 are available at http://www.ar.embnet.org/downloads. New features in wEMBOSS 1.6.0 include compatibility with new data types in EMBOSS 3.0.0 and improved conversion of ACD expressions to Perl. Changes in wrappers4EMBOSS include new gap penalty parameters.

People in the News

Arthur Holden has joined Illumina as senior vice president of corporate and market development, a new position. Holden was most recently chairman, CEO, and principal founder of First Genetic Trust, which ceased operations last year (see story, this issue). He will serve as Illumina's representative on the Personalized Medicine Coalition and also help lead content development strategies for the company's products. Holden is chairman of the Pharmaceutical Biomedical Research Consortium and the DMD Translational Research Consortium and was formerly CEO of the SNP Consortium and CEO and a director of Celsis International.


The US Department of Health and Human Services said this week that David Brailer has resigned as national coordinator for health information technology, a position he has held since the post was created in 2004. Brailer will serve as vice-chair of the American Health Information Community, which is charged with making recommendations to the HHS secretary to "facilitate the development and adoption of standards-based health IT," HHS said. A replacement for Brailer has not yet been named.


Rick Stevens has been appointed associate laboratory director for computing and life sciences at the US Department of Energy's Argonne National Laboratory. The newly created directorate brings together two Argonne research divisions -- the Biosciences Division and the Mathematics and Computer Science Division -- along with two new divisions -- the Computation Institute and the Institute for Genomics and Systems Biology. Al Sattelberger, formerly associate laboratory director for physical biological and computing sciences, is now associate laboratory director for physical sciences. Stevens has been at Argonne since 1982, and has served as director of the Mathematics and Computer Science Division and also as acting associate laboratory director for physical, biological, and computing sciences. He is currently leader of Argonne's Petascale Computing Initiative. From 2000-2004, Stevens served as director of the National Science Foundation's TeraGrid Project and from 1997-2001 as chief architect for the National Computational Science Alliance. Kevin White has been appointed director of the new Institute for Genomics and Systems Biology -- a joint initiative between the University of Chicago and Argonne "to further expand resources and capabilities in the emerging areas of integrative biological research." White joins Argonne from Yale University, where he served as director of applied genomics at the Yale Center for RNAi and Therapeutic Chemical Genetics, associate professor of genetics at the Yale University School of Medicine, and associate professor of ecology and evolutionary biology.

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