Generic Model Organism Database Project / News: Recent posts

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.) ... read more

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.... read more

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.... read more

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.

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 :-)... read more

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.... read more

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
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.... read more

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.... read more

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>.... read more

From an email sent to the gmod-announce mailing list by Arek Kasprzyk:

BioMart 0.5, a new version of the query-oriented data management system
has been released. The new release comes with a number of new features
and
improvements:

MartView

BioMart web code has been re-implemented in order to make it easier to
set
up and run queries. Filters and attributes now come in collapsible
panels,
considerably improving the scalability of the interface. The handling of
two dataset queries has been much improved. It is now possible to
combine
attributes as well as filters in such queries which makes it possible to
fully annotate a local dataset with a remote one. Customization of
options
including colour schemes, result file handling, logging options etc is
much easier to manage in the new code. Finally it is now possible to use
the webcode with apache 2 as well as apache 1.... read more

From an email to the gmod-annouce mailing list by Brian Osborne:

GMOD and Apollo lists,

My name is Brian Osborne, and I'm writing to introduce myself and the newly
created GMOD Help Desk. Some of you may know me as a participant in Bioperl
where I've been contributing code, documentation, and general support for a
number of years. This Help Desk position, lasting about 3 years, is funded
by a grant written by leaders of GMOD and NESCent, the National Evolutionary
Synthesis Center.... read more

I am pleased to announce that there will be a GMOD meeting following the Plant and Animal Genome meeting in January. The GMOD meeting will be
held on January 18 and 19 at the Town and Country Hotel in San Diego's Hotel Circle. I do not yet have registration information but that should be forthcoming soon.

Two anticipated agenda items for the meeting are 'bake-offs', where different ways of achieving a goal are considered. One of the bake-offs will be a model organism database bake off, where any MOD that would like to participate will demonstrate how a redetermined set of questions would be answered using the her MODs web interface. Please let me know if you are interested in articipating.... read more

I am unbelievably happy to announce that GBrowse 1.65 has been released. There have been several improvements since the 1.64 release. Here is a
snippet of our Change file:

* Improved support for negative and fractional coordinates, such as those used
in some genetic maps.
* Added fixes to GFF.pm for GFF3 to BioPerl patches
* Fix the way that plugins are stored in mod_perl environment to prevent them from
appearing and disappearing haphazardly when switching between sources.
* Added a trace glyph
* Several fixes to the Chado adaptor, mostly to keep up with changes
to APIs... read more

Hi everyone,

Version 0.16 of CMap has been released.

You can get the new version from SourceForge,
http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129&release_id=424666.

If you have any questions, please let me know.

Changes include:
- Updated menus to be more intuitive
- Added AJAX to load the comparative maps menu separately to speed up
page
loading
- Added more options to opening menu
- Caches the first view of a map (before sessions are invoked)
- Removed cluster correspondence option
- Bug fixes
- Added chado synchronization tools
- Added commas to the matrix
- Some query optimization
- Added script to order, orient and stack relational maps based on a
reference map for easier viewing
- Allow for custom map size
- Modified the make name correspondence code to work with really large
maps
- Modified the delete duplicate correspondence code for speed
- Allow for multiple installations on the same machine... read more

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Hello,

Since SourceForge and my ISP were having difficulties at the time I
initially posted this announcement, I wanted to post it again in case it
was missed by anybody. Also, I have a few items to add:

- The deadline to be sure to get the GMOD meeting rate at the hotel is
May 29. It may be possible to get the meeting rate after then, but
there are no guarantees.... read more

Hi Everyone,

We are announcing a new Sourceforge Project called Modware that may be of
interest to you. It is an object-oriented API written in Perl that
creates in-memory object representations of biological features stored in a
Chado database.

For download please visit our Sourceforge project page:
http://sourceforge.net/projects/gmod-ware

For API documentation and some short examples of selected use cases visit
our project home page:
http://gmod-ware.sourceforge.net/... read more

Hello,

I am pleased to announce that the semi-annual GMOD meeting will be held
a the National Evolutionary Synthesis Center <http://www.nescent.org/>
in Durham, NC on June 29 and 30. In addition to 'typical' topics for
discussion (new applications, progress on making applications
interoperate), we will discuss how existing applications can be used or
modified for evolutionary biologists and what applications could be
developed in conjunction with GMOD to facilitate evolutionary model
organism databases. I am also accepting suggestions for topics or
talks.... read more

Dear colleagues,

The new modENCODE project (http://www.genome.gov/ENCODE/#modEncode)
will be a boon to model organism functional genome data, and I'd like
to join with others in collaborating or consulting on the data
coordination center planned for this research network.

This would be in my view an excellent way to prove and improve the
computational tools of GMOD's Generic Model Organism Database
framework, as well as build a fully operational data center for large
scale functional elements in C. elegans and/or D. melanogaster.... read more

A new BioMart web server has been set up in order to keep
an up to date record of public datasets available in the BioMart format.
If you would like your site to be included please send us an email and
we'll
hyperlink it from www.biomart.org and include any additional information
e.g. pointers to database dumps etc.

If you are running version 0.4 we'll also be able to redirect to
MartService
on your site through our MartView (www.biomart.org/biomart/martview)
and and/or MartService
(www.biomart.org/biomart/martservice?type=registry).... read more

BioMart 0.4, a new version of the query-oriented data management system
has been released. This release includes the following new features:

It is now possible to federate BioMart databases over port 80 which
overcomes any issues with direct RDBMS access and permits the use of
BioMart remotely without the need to either expose database servers to
the outside world or open outgoing connections through a firewall.
This new feature takes advantage of the web service layer which has now
been exposed to third party programmers.... read more

Dear Genome miners,

Find this tool of interest if you have piles of genome GFF annotations
that you want a better way to sift through:

gff2biomart.pl -- create tables for BioMart from genome GFF annotations

The script generates table .sql, .txt and .xml suited to BioMart
(MySQL, BioMart version 0.3 tested). It is a simple script without
special requirements, basically a data transformer that writes new
files formatted for a BioMart database. ... read more

++++++++++++++++++++++++
+ ANNOUNCEMENT +
++++++++++++++++++++++++

The NeuroScholar system is a general purpose knowledge management system for
the biomedical-literature. It permits users to build an organized library of
PDF files and then make and manage free-form notes based on the articles.
This simple functionality is the first phase of the creation of a system
that enables experimental biologists to construct knowledge bases of what
they know. This is an attempt to introduce an informatics framework into the
lab to facilitate to an increased level of formalism in terms of
mathematical representation to the subject. ... read more

Hey all,

Version 0.02 of balstGraphic module has been released.

You can get the new version from SourceForge,

http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=101505

Changes include:

--------
1. Removed the extra 2s on the display along the bottom of the graphic
that shows the e-value ranges for the different colors. Thanks to
Jon Slenk <jonslenk@acoma.stanford.edu> and Evan Herbst
<evh4@cornell.edu> for reporting the bug and providing the fix.... read more

Hello,

I am pleased to announce, after much anticipation, the release of the
Generic Genome Browser (GBrowse) version 1.64. There have been several
changes since the last public release, version 1.62, which are detailed
below. The release can be obtained from the GMOD/SourceForge download
page at:

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

Here is the change log since version 1.62:... read more