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MassLynx 4.1, GenBank 148.0, Reactome, Genome Browser, StARLITe, DrugStore, MySQL, Oracle, Postgres, Wildfire 2.0, Nautilus, Taverna 1.2, Alan Williamson, Charlie Lieu, Jason Stajich and more

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Waters has released MarkerLynx db Application Manager, a metabonomics and biomarker data management tool for its MassLynx 4.1 statistical analysis and database searching software. MarkerLynx db Application Manager offers improved peak detection, enhanced statistical tools, and new dynamic database searching and storage capabilities for the identification of biomarkers, the company said.


GenBank 148.0 is now available from the National Center for Biotechnology Information at ftp://ftp.ncbi.nih.gov/. The release contains 49,398,852,122 base pairs and 45,236,251 entries. Uncompressed, the 148.0 flat files require about 172 GB for the sequence files only. The ASN.1 version requires around 148 GB.


Reactome version 14 is available at http://www.reactome.org. New modules and subsections include post-translational modification of proteins, notch signaling, and hormone-sensitive lipase added under lipid metabolism; mitochondrial transcription added under transcription; MAPK cascade added under insulin receptor mediated signaling; and polo-like kinases added under cell cycle, mitosis.


The University of California Santa Cruz Genome Bioinformatics Group has released a Genome Browser for the Drosophila simulans draft genome sequence. The total size of the assembly is 142,405,747 base pairs including gaps and 127,241,461 base pairs excluding gaps. Downloads of the droSim1 data and annotations are available at ftp://hgdownload.cse.ucsc.edu/goldenPath/droSim1/.


Inpharmatica has launched two new drug discovery databases: StARLITe and DrugStore. StARLITe, a chemogenomics database, contains reported screening information for more than 300,000 compounds, their molecular targets, and their biological activities. DrugStore is a knowledgebase of information on all FDA-approved drugs.


The Medical University of South Carolina has released ArrayQuest, a web-based program for analyzing DNA microarray data, at http://proteogenomics.musc.edu/quickSite/musc_madb.php?page=home&act=manage. The software suite includes four modules: µArrayDB, a program for archiving DNA microarray data derived from experimentation; an ArrayQuest analysis module, which allows a client to select microarray information from the µArrayDB database for analysis; an analysis job-distribution module, which sends an analysis job to a CPU within a backend analysis cluster that is ready to accomplish the job; and an upload module, which enables off-site clients to import data into µArrayDB or to a private database.


The European Bioinformatics Institute has released version 3.0 of its BioMart data management system, which supports MySQL, Oracle, and Postgres, at http://www.ebi.ac.uk/biomart/install.html.


Singapore's Bioinformatics Institute has released Wildfire 2.0, a GUI application for constructing workflows, at http://wildfire.bii.a-star.edu.sg. The software has been configured to build workflows using EMBOSS applications, which can run on a cluster or other multi-CPU machine.


Thermo Electron has released version 7.0 of its Nautilus LIMS for early-stage discovery. Nautilus includes a new archiving function that enables users to automatically transfer data from active tables to archived tables and back again.


Taverna 1.2 is available at http://taverna.sf.net. New features include support for BioMart and BioMoby, and a new semantic service discovery tool called Feta.

People in the News

Genstruct has appointed Alan Williamson to its scientific advisory board and has hired Charlie Lieu as director of business development and marketing.

Williamson is a former member of the advisory council to the National Human Genome Research Institute and is currently a member of NHGRI's sequencing and HapMap advisory panels. Before retiring from full-time employment, he was a professor of biochemistry at the University of Glasgow before holding senior research management positions at Glaxo and Merck. In 1994, he initiated and directed the Merck Gene Index Project, and in 1998-99, he coordinated the creation of the SNP Consortium.

Lieu has served as technology analyst and corporate liaison for Merck Research Labs and also managed technical marketing and sales for Merck subsidiary Rosetta Inpharmatics.


Jason Stajich has been elected president of the Open Bioinformatics Foundation, a non-profit organization that provides administrative support for BioPerl, BioJava, BioPython, and several other open source bioinformatics projects. OBF's board of directors elected Stajich, a graduate student in genetics at Duke University and a core developer for the BioPerl project, to the position last week during the OBF's annual Bioinformatics Open Source Conference.

Stajich succeeds Ewan Birney of the European Bioinformatics Institute, who resigned after serving as president since the OBF was founded in 2001. Birney will remain on the OBF's board of directors as a board member at large, along with Steven Brenner of the University of California, Berkeley, another founding member of the OBF. Other OBF officers include Andrew Dalke, of Dalke Scientific Software, who serves as secretary; Chris Dagdigian of the BioTeam as treasurer; and Hilmar Lapp of the Novartis Research Foundation as parliamentarian.

The OBF board also passed new bylaws that will open up the organization to a broader membership that will vote for officers in future elections.

Filed under

The Scan

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Genome Biology Papers Present Epigenetics Benchmarking Resource, Genomic Architecture Maps of Peanuts, More

In Genome Biology this week: DNA methylation data for seven reference cell lines, three-dimensional genome architecture maps of peanut lines, and more.