GMOD news items are now published directly on the GMOD web site at
News is also available as an RSS feed
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@..., or to me personally at clements@... 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.
GMOD Help Desk
2007-12-14 12:06:43 PST by scottcain
I am pleased to announce that the registration page for the November
2007 GMOD meeting is now available. You can find it at
and more information about the meeting can be found at
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 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@.... Please accept my apologies for
multiple copies of this email that you may have received.
2007-10-08 09:03:35 PDT by scottcain
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.
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...]
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 ...]
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@... with the project code in the subject line. Please include a cover letter, resume, and contact information with
2007-05-03 15:35:25 PDT by scottcain
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 15:50:06 PDT by lstein
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 http://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 http://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.
2007-04-12 12:50:40 PDT by scottcain