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Project News for Generic Model Organism System Database

  • GMOD news and RSS feed on www.gmod.org

    Hello all,

    GMOD news items are now published directly on the GMOD web site at

    http://gmod.org/wiki/index.php/GMOD_News

    News is also available as an RSS feed

    http://gmod.org/wiki/index.php?title=GMOD_News&action=feed&feed=rss

    Selected news items will be linked to from the News section of the GMOD home page, http://gmod.org.

    If you have a news item of interest to the GMOD community please e-mail it to the GMOD Help Desk at help@gmod.org, or to me personally at clements@nescent.org and we will post it to the web site. (Or, you can add it to the wiki yourself.)

    The GMOD News section at SourceForge (what you are reading right now) is now deprecated, and may go away at some point in the future.

    Please let me know if you have any questions.

    Thanks,

    Dave Clements
    GMOD Help Desk

    2007-12-14 20:06:43 UTC by scottcain

  • Registration for the November GMOD meeting

    Hello,

    I am pleased to announce that the registration page for the November
    2007 GMOD meeting is now available. You can find it at

    http://blog.gmod.org/register.html

    and more information about the meeting can be found at

    http://www.gmod.org/wiki/index.php/November_2007_GMOD_Meeting

    Note that the above link is a wiki page; if there are items you would
    like to see discussed at the meeting, please feel free to add them to
    the page.

    The GMOD meeting will take place at Cold Spring Harbor Laboratory on
    November 5, 1:30PM to November 7 noon, which follows the Genome
    Informatics meeting that runs from November 1 to November 5.

    Please direct any follow up questions to the GMOD-devel list, at
    gmod-devel@lists.sourceforge.net. Please accept my apologies for
    multiple copies of this email that you may have received.

    Scott

    2007-10-08 16:03:35 UTC by scottcain

  • Berkeley GMOD (et al.) needs people

    We're hiring. It's gone from bust to boom in the space of a few months, and now we're scrambling to get 3 new people on board.

    from all of us at Berkeley... Suzi Lewis, Chris Mungall, Seth Carbon, John Day-Richter, Mark Gibson, Karen Eilbeck, & Nicole Washington

    Software Developer positions in Berkeley: http://berkeleybop.org/content/jobs/

    The Berkeley Bioinformatics and Ontologies Project (BBOP, http://berkeleybop.org), located at Lawrence Berkeley National Laboratory
    (LBNL), is seeking three software developers to craft tools for the collection, annotation, and integration of biomedical data. The BBOP
    is a founding member of the Gene Ontology Consortium, and a part of the National Center for Biomedical Ontology. We have a long history
    developing open source software and databases for Drosophila and other model organisms, and are an original member of the Generic Model Organism Database (GMOD) project. We are an extremely
    collaborative team that is built upon the creative sharing of ideas among bright individuals.

    1. modENCODE
    The applicant will work on an important new project, modENCODE, whose aim is to discover and explore the genomes of C. elegans and D.
    melanogaster , using new scientific strategies and new technologies for discovery. It is a collaborative project with Cold Spring Harbor
    Laboratory, Cambridge University, University of California Santa Cruz. The applicant will be responsible for collecting and collating
    experimental data from many different sources. [see http://berkeleybop.org/content/jobs/modENCODE.shtml for more...]

    2. NCBO/BIRN
    The applicant will work on an important new collaboration between the National Center for Biomedical Ontologies (NCBO) and the Biomedical
    Informatics Research Network (BIRN). The BIRN, based at the University of California San Diego, is an initiative within the National Institutes of Health that fosters large-scale collaborations
    in biomedical science by utilizing the capabilities of the emerging cyberinfrastructure. BIRN is targeting advances in understanding the
    genetics of human disease by identifying correlations between genetic insults and neuropathological processes. The database mediation software will support ontological query and retrieval of image information based on phenotypic descriptions. Our role is to assist
    in building the requisite data and knowledge stores, by building ontology-directed graphs for query navigation. [see http://berkeleybop.org/content/jobs/BIRN.shtml for more ...]

    3. APOLLO
    The applicant will work on an important software component of the GMOD project: Apollo. Apollo allows researchers to explore genomic
    annotations at many levels of detail, and to perform expert curation of the genome, all within a graphical environment. Our role is to support the global users of Apollo and to extend its capabilities in numerous ways. The Apollo project is a joint collaboration between LBNL and the Arabidopsis Information Resource (TAIR), located at Stanford. [ see http://berkeleybop.org/content/jobs/Apollo.shtml for more ...]

    How to Apply
    Applications and questions may be sent to Nicole Washington nlwashington@lbl.gov with the project code in the subject line. Please include a cover letter, resume, and contact information with
    your application.

    2007-05-03 22:35:25 UTC by scottcain

  • GBrowse 1.68 Released

    Version 1.68 is a stability release which improves the documentation and installation process. It includes a new script called gbrowse_netinstall.pl, which will semi-automatically install GBrowse across the Internet on Windows, Mac OSX and Linux platforms. For me details, see the GBrowse WIKI page at http://www.gmod.org/wiki/index.php/GBrowse.

    2007-04-17 22:50:06 UTC by lstein

  • New gmod.org website

    Thanks to many weeks of work by Brian Osborne and several others, there
    is a new GMOD wiki <http://wiki.gmod.org/> that is poised to become the
    new www.gmod.org. The old site (the one powered by Drupal) will remain
    as http://blog.gmod.org/ and I will continue to use it to write weekly
    progress reports, and I encourage others to do the same, to facilitate
    writing longer progress reports when necessary (and it always is :-)

    I have worked for a while writing Apache mod_rewrite rules so that most
    URLs that currently work will continue to work when the change takes
    place. If you find non-working URLs, please let me know so I can fix
    them. Typically, if I don't have a specific rule for a given url, you
    will get the 'You can create this page' in wiki, and you can feel free
    to do exactly that if you think it is necessary.

    During the transition, some requests for www.gmod.org URLs may resolve
    to gmod.cshl.edu, which is the name of the server that is hosting the
    wiki. This should be a transient issue and will go away after the DNS
    requests have propagated around the world.

    Finally, about accounts: currently, you must have an account to edit
    pages on the wiki, but accounts are given out freely. While we have not
    really done much advertising of this site, it has already gotten some
    wiki-spam, so I suspect at some point in the near future we will require
    users to ask for an account and then the request will be granted by
    someone with admin privileges.

    Happy wiki'ing!
    Scott

    2007-04-12 19:50:40 UTC by scottcain