Downloads & Upgrades
The National Center for Biotechnology Information has released Blast 2.2.13. Changes include a new engine in blastall that enables multiple queries at once and accelerates large queries; improved statistical parameters for megablast, blastall, and bl2seq; and several bug fixes. NCBI has also released the NCBI Search Toolbar, which allows users to search NCBI databases using a local toolbar, at http://www.ncbi.nlm.nih.gov/projects/toolbar/. In addition, RefSeq 14, which includes 2,135,138 proteins and sequences from 3,198 organisms, is available at ftp://ftp.ncbi.nih.gov/refseq/release/. Finally, NCBI has released GenBank 151.0 at ftp://ftp.ncbi.nih.gov/. The release contains 56,037,734,462 base pairs and 52,016,762 entries. Uncompressed, the 151.0 flat files require about 196 GB for the sequence files only. The ASN.1 version requires around 170 GB.
The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the VisiGene Image Browser at http://genome.ucsc.edu/cgi-bin/hgVisiGene. VisiGene enables users to view in situ images in order to examine expression patterns at both the tissue and cellular levels. The initial release of VisiGene includes mouse in situ images from the Jackson Laboratory Gene Expression Database, transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology, mouse head and brain in situ images from NCBI's Gene Expression Nervous System Atlas database, and Xenopus laevis in situ images from the National Institute for Basic Biology XDB project. The UCSC team said it also plans to add images from the Allen Brain Atlas to the VisiGene collection.
Elsevier MDL has released the initial version of its MDL Notebook electronic lab notebook, which allows scientists to store experiment protocols, share hypotheses with colleagues, and legally document discoveries.
MiraiBio, a division of Hitachi Software Engineering America, has released MasterPlex QT v2.5, quantitation software for statistical analysis of multiplexed data generated on the Luminex 200 liquid array detection system. The software includes multi-sample charts, three-dimensional depth charts, and intensity maps and is able to generate weighted four- and five-parameter logistics standard curves, dose- response curves, and residual plots.
The National Cancer Institute and Fred Hutchinson Cancer Research Center have released version 1.1 of the Computational Proteomics Analysis System (CPAS), an open-source web-based software platform that includes tools for organizing, managing, processing, and interpreting proteomics data. Further information is available at https://cabig.nci.nih.gov/workspaces/ICR/CPAS/document_view.
Taverna 1.3.1 is now available at http://taverna.sourceforge.net. The release includes improvements in interface performance and diagram generation, includes a tool called interaction service, which enables service providers to allow human interaction within workflows.
The University of Michigan has released Merlin 1.0.1 at http://www.sph.umich.edu/csg/abecasis/merlin. New features include enhanced haplotype output that tracks the segregation of each founder chromosome through a pedigree.
The Laboratory for Optical and Computational Instrumentation at the University of Wisconsin, Madison, has released OME-TIFF, a format that adapts the OME-XML (Open Microscopy Environment XML) specification into a TIFF-based solution, at http://www.loci.wisc.edu/ome/ome-tiff.html.
People in the News
Tripos has appointed Kathleen Mensler as vice president of marketing and corporate development for its Discovery Informatics business and Tom Mander as vice president of business development and strategic alliances for its Discovery Research business. Mensler most recently served as vice president of business development at Elsevier MDL, where she also held executive-level positions in marketing, product development, and business management. Prior to joining MDL, Mensler worked as a medicinal chemist at Merck. Mander comes from Evotec, where he served in a number of roles, including department manager, product manager and vice president of business development. Before joining Evotec, Mander was a group leader at Glaxo Wellcome (now GlaxoSmithKline), and held senior scientific roles at Xenova, the Center for Natural Product Research (now MerLion) and Amersham International (now GE Healthcare).
Jeffrey Skolnick is leaving his position as director of the Buffalo Center of Excellence in Bioinformatics at SUNY-Buffalo to join the Georgia Institute of Technology as the Georgia Research Alliance Eminent Scholar in Computational Systems Biology. According to a Georgia Tech press release, Skolnick will bring 19 research scientists and technicians "and more than $1.5 million in federal funding" to the university. Skolnick and his team will be housed in the School of Biology, a unit in the College of Sciences.
Kenneth Buetow has been appointed to the new position of Associate Director for Bioinformatics and Information Technologies at the National Cancer Institute, according to a recent NCI Cancer Bulletin. Buetow was previously director of the NCI Center for Bioinformatics. In his new position, Buetow will "manage and execute information technology and bioinformatics initiatives that will lead to the usage of common tools, standards, and datasets across NCI; assist internal teams in adopting and leveraging NCI's cancer Biomedical Informatics Grid (caBIG) infrastructure; review and update NCI's existing and planned bioinformatics programs and activities; make recommendations for the creation of a standing group that will provide technical guidance on new projects; and regularly report to the NCI Executive Committee, of which he is a member," the Cancer Bulletin said. An NCI spokesperson could not confirm before press time whether the institute plans to appoint a new director for the NCICB.
The Biosystems Informatics Institute has appointed David Flanders as chief operating officer. Flanders most recently served as head of basic technologies at Lion Bioscience. He has a PhD in cell and development biology from Australian National University and a BSc in agricultural botany from the University of Newcastle-upon-Tyne.
The National Center for Genome Resources has hired Gregory May as leader of its nutritional biology program, Jim Huntley as a senior research scientist, and Steven Day as director of software engineering. May was associate scientist and head of the Medicago Genomics Program at the Samuel Roberts Noble Foundation, and assistant scientist at the Boyce Thompson Institute for Plant Research at Cornell University. Huntley was most recently an assistant professor at New Mexico Highlands University and director of the NMHU Research Infrastructure in Minority Institutions program. Day was previously director of information technology at the Molecular Profiling Institute and also led the software engineering unit within the Translational Genomics Research Institute and worked for SRA International.