GMOD news and RSS feed on www.gmod.org

ian holmes — Fri, 14 Dec 2007 20:06:43 -0000

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

Registration for the November GMOD meeting

ian holmes — Mon, 08 Oct 2007 16:03:35 -0000

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

Berkeley GMOD (et al.) needs people

ian holmes — Thu, 03 May 2007 22:35:25 -0000

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.

GBrowse 1.68 Released

ian holmes — Tue, 17 Apr 2007 22:50:06 -0000

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.

New gmod.org website

ian holmes — Thu, 12 Apr 2007 19:50:40 -0000

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

Pathway Tools Tutorial June 4-8

ian holmes — Wed, 04 Apr 2007 17:47:22 -0000

Pathway Tools Tutorial June 4-8, 2007

SRI's Bioinformatics Research Group will be holding a Pathway Tools
tutorial session on June 4-8, 2007 at SRI International in Menlo
Park, CA.

The goal of the tutorial is to teach scientists how to use the Pathway
Tools software to create a Pathway/Genome Database (PGDB) for an
organism of interest, how to interactively update and curate a PGDB,
and how to publish a PGDB on the web, and how to use the Pathway
Tools omics viewers.

Pathway Tools includes a unique combination of bioinformatics
algorithms including a predictor of metabolic pathways, an operon
predictor, and an algorithm for predicting which genes in a genome
code for missing enzymes in predicted metabolic pathways ("pathway
holes").

Each day's tutorial will last from 9:30am-5:00pm. Each day will
combine lectures with lab sessions in which students apply the
software to a sample genome. No programming experience is required
for days 1-4, but a basic knowledge of Unix is helpful, as is
knowledge of a Unix text editor such as vi or emacs.

Day 5 requires programming experience in Perl, Java, or Lisp. Day 5
is optional.

Three example PGDBs are:

o EcoCyc http://EcoCyc.org/
o Yeast pathway database: http://pathway.yeastgenome.org/biocyc/
o Arabidopsis pathway database: http://www.arabidopsis.org/biocyc/index.jsp

Agenda:

Day 1 (June 4)
Introduction to Pathway Tools
Overview of Pathway/Genome Navigator
Pathway Tools Omics Viewers: Cellular Overview, Regulatory Overview, Genome Overview
Querying PGDBs with BioVelo

Day 2
Pathway prediction using PathoLogic
Matching enzyme names to reactions
Pathway hole filler

Day 3
Operon predictor
Pathway Tools schema
Administering Pathway Tools
Pathway/Genome Database Registry

Day 4
Transport Inference Parser
Editing Pathway/Genome Databases

Day 5 (optional)
The Pathway Tools APIs -- Programmatic querying and updating of PGDBs
using the Perl, Java, and Lisp languages.

If you wish, you may bring with you to the tutorial the annotated
genome of an organism for which you wish to build a PGDB, in which
case you will most likely leave the tutorial with a draft version of
the database.

Please reply to Wilma Lenz (lenz@ai.sri.com) to reserve a space at the
tutorial; space is limited. There will be a tutorial fee of $75 to
cover food and other expenses. Please indicate if you will attend Day 5.

For more information about the tutorial please see:

http://bioinformatics.ai.sri.com/tutorial/

Peter Karp
Bioinformatics Research Group
SRI International

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Gmod-announce mailing list
Gmod-announce@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gmod-announce

GBrowse 1.67 released

ian holmes — Tue, 06 Mar 2007 19:37:58 -0000

Version 1.67 of the Generic Genome Browser (GBrowse) has been released. This version adds support for embedding tables of related tracks inside the track selection section, and fixes bugs in the DAS support. Download it here: http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513. 1.67 now]</a>.

2nd International Biocuration Meeting

ian holmes — Tue, 20 Feb 2007 23:52:15 -0000

2nd International Biocuration Meeting
October 25-28, 2007
Dolce Hayes Mansion, San Jose, California, USA

Purpose:
The goal of this meeting is to provide a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this important and rapidly growing area of research.

Registration, lodging, and abstract submission are now open. The abstract submission deadline is July 1, 2007.

For more information, please see the meeting web site at:

http://biocurator.org/Mtg2007/

The meeting organizers would like to thank the Genetics Society of America, the National Science Foundation, the Klaus Tschira Foundation, and Bioneer for their support.

The First Biocuration Meeting was a great success. We look forward to your participation in the second meeting!

Organizing Committee:
Maria Costanzo
-Saccharomyces and Candida Genome Databases, Stanford University, USA
Petra Fey
-dictyBase, Northwestern University, USA
Takashi Gojobori
-Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Japan
Win Hide
-South African National Bioinformatics Institute, University of the Western Cape, South Africa
David Hill
-Mouse Genome Informatics, USA
Doug Howe
-Zebrafish Information Network, University of Oregon, USA
Renate Kania
-Scientific Databases and Visualization, EML Research gGmbH, Germany
Sue Rhee
The Arabidopsis Information Resource, Carnegie Institution, USA
Mary Schaeffer
-USDA ARS , MaizeGDB and University of Missouri, USA
Susan St. Pierre
-Flybase, Harvard, USA
Simon Twigger
-Rat Genome Database, Medical College of Wisconsin at Milwaukee, USA
Owen White
-The Institute for Genomic Research, USA

Version 1.66 of GBrowse now available

ian holmes — Thu, 07 Dec 2006 17:59:30 -0000

From an email sent by Scott Cain to the GMOD Announce mailing list:

Hello,

I am pleased to announce that version 1.66 of GBrowse is now available.
Considerable thanks are due to Lincoln and other GBrowse developers and
as well to the many developers working on BioPerl, but most especially
to Sendu Bala for shepherding the release of BioPerl 1.5.2 (released
yesterday), which is required for GBrowse 1.66.

This release marks the first time an installer script for Windows is
included; to get the install script, go to:

http://www.gmod.org/gbrowse/windows

and follow the directions.

GBrowse can be downloaded from SourceForge at:

http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513&release_id=469470

Here is a change log for this release:

1.66 * Added files from SynView to the contrib directory; these files
include a GUSdb adaptor and configuration files and sample
data for a 'in-gbrowse' synteny viewer.
* Added support to Chado adaptor to respect the reference class
in the conf file (previously, the adaptor would infer the
reference class from the database structure). If the
reference class is not provided in the database, the old
behavior still works. Thanks to Emmanuel Quevillon for
the patch that implements this change.
* Improved support in Chado adaptor for inferring CDS and UTR
features from exons and polypeptides (at the expense of speed).
* Added support to the Chado adaptor for showing alignments with
sequence residues in the display panel as well as gbrowse_details.
* Added a visual test for verifying that images produced by GBrowse
agree with what is in the tutorial.
* Fixed a bug in the CAlign module for doing alignments.
* Fixed several minor bugs that were inadvertanly included in the
1.65 release.
* CGI now produces valid XHTML 1.0.
* Added the ability to use a callback as a citation.

Happy Browsing!
Scott

January 2007 GMOD meeting registration

ian holmes — Tue, 05 Dec 2006 04:34:19 -0000

The registration page for the GMOD meeting is now available at

http://www.gmod.org/meeting_registration

Note that there is no registration fee for this meeting, though there is a limit of 50 attendees.

The agenda is shaping up quite well: the User Interface Caucus <http://www.gmod.org/user-interface-caucus> will take place on day one of the meeting and the Chado middleware API will be on day 2 <http://www.gmod.org/middleware-bake-off>.

See you in January!
Scott

Recent posts to news