Generic Model Organism Database Project / News: Recent posts

Flash GViewer - version 0.4

Version 0.4 of the Flash Genome Viewer tool is now available for download on sourceforge:
http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=161280

Introduction: Flash GViewer is a customizable Flash movie that can be
easily inserted into a web page to display each chromosome in a
genome along with the locations of individual features on the
chromosomes. It is intended to provide an overview of the genomic
locations of a specific set of features (See http://rgd.mcw.edu/diseases/ for working example).... read more

Posted by Scott Cain 2005-11-30

CMap 0.15 released

Hi everyone,

Version 0.15 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=371937.

If you have any questions, please let me know.

Changes include:

- Server side sessions are used to store the information about what is
being viewed. This dramatically reduces URL size and allows more
complex operations. However, sessions expire, making bookmarks
volatile.
- Added a feature to save links permanently. By clicking the "Save
Link" button, a new permanent URL is created for the user to bookmark.
Saved links can also be browsed.
- "Saved Links" can also be imported via cmap_admin.pl using an XML
file.
- The "Import Links" code has been completely replaced by "Saved
Links" code. The "Import Links" code created links that were easily
deleted by the system and didn't have a very robust import format.
- A "Hide Empty Rows" option was added to the matrix.
- Speed increases to help with larger data sources.
- Allow individual "Minimum number of Corrs" value for each slot.
- Added a "default" feature type display value for features that may
be on new comparison maps.
- Added a cluster correspondence option.
- Each slot only has one title box, with slot specific buttons in it.
- Each map has it's own set of buttons on the image.
- Allow individual maps in slot to be deleted using the button labeled
"x".
- Allow the maps in a slot to be limited to an individual map using
the button labeled "L".
- Allow individual maps in slot to be flipped. The flip button for
flipped maps is labeled "UF" for un-flip.
- Allow maps of different base units to be scaled using a conversion
factor specified in the config file.
- A "clean view" is now offered that does not have the navigation
buttons on the picture. This is to make the image more appealing for
publishing.
- Reference maps can be stacked vertically or placed in multiple rows.
- The order of the reference maps can be specified.
- Intra-slot correspondences can be displayed.
- A "Spidering" feature has been created to allow you to see how a map
is related to other maps in its map set. The spider crawls the
intra-slot correspondences to a selected depth. It returns an image
with a row of maps for each level.
- Option to draw correspondence lines to either the features or the
maps.
- Option to turn off some or all of the clickable elements on the
image to save bandwidth and render time.
- Sanity check for the number of clickable elements on an image.
- All database queries have been moved to a single module.... read more

Posted by Scott Cain 2005-11-19

New GMOD website

Hello,

I am pleased to announce the roll out of the new GMOD website,
http://www.gmod.org/ . This website uses content management software,
Drupal, to facilitate user input. While the porting of the data on the
old GMOD website ( http://gmod.sf.net/ ) is not quite done, it is nearly
there. Please take a look at the new website and feel free to leave
comments.

I don't want to spend too much time 'explaining' the website, as I hope
it explains itself, but I do want to point out that the central piece of
content on the site is a section called 'Components'. In Drupal speak,
this is a book, but really is a hierarchical set of pages where
information about various GMOD software components. Drupal facilitates
group content development, so anyone with an account will be able to
edit content in the Components book. The Components book takes the
place of the 'software matrix' on the old web site.... read more

Posted by Scott Cain 2005-11-18

PuMA: a tool for enhanced PubMed search

http://metnetdb.gdcb.iastate.edu/browser

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Posted by Scott Cain 2005-10-29

Please take the Gene Ontology survey

Hello,

The Gene Ontology (GO) is a system for functional annotation of genes and
gene products. It enables classification of gene products according to
molecular function, biological process, and cellular location of
action.

Please help us by taking part in our survey.

The results of this survey will help us improve our services
to our user community, and help direct our resources more effectively.... read more

Posted by Scott Cain 2005-10-28

pg_dump files for chado-0.003

Find them here:

https://sourceforge.net/project/showfiles.php?group_id=27707&package_id=167771

These were produced using postgresql-7.4.7-3.FC2.1. Let me know if there
are problems.

-Allen

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Posted by Scott Cain 2005-10-28

Draft agenda for October GMOD meeting

Hello,

Below is a draft version of the agenda for the upcoming GMOD meeting.
First a few comments:

* Please follow up with comments and questions to the gmod-devel
mailing list, and the registered attendees will be receiving a separate
copy of this mailing.

* The agenda is somewhat loose on purpose; I want to encourage lots of
discussion and leave room for topics I haven't thought of.

* While I indicated that there would be no 'show and tell' like
previous meetings, I do think there is room for actual, working software
demos. Let me know if you have something you would like to show off.... read more

Posted by Scott Cain 2005-10-24

Biocurator Meeting: registration/abstract deadline soon

** Registration and Abstract deadline October 11 **
First International Biocurator Meeting, Asilomar, CA, December 8-11, 2005

The goal of this meeting is to create a forum for curators and developers of
biological databases to discuss their work, promote collaborations, and foster
a sense of community in this very active and growing area of research.
Confirmed plenary speakers include:
-Rolf Apweiler (EBI)
-Russ Altman (Stanford University)
-Mike Tyers (Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto).... read more

Posted by Scott Cain 2005-09-30

First International Biocurator Meeting, Asilomar, CA, Dece

** Second announcement **
First International Biocurator Meeting, Asilomar, CA, December 8-11, 2005

The goal of this meeting is to create a forum for curators and developers of
biological databases to discuss their work, promote collaborations, and foster
a sense of community in this very active and growing area of research.
Confirmed plenary speakers include:
-Rolf Apweiler (EBI)
-Russ Altman (Stanford University)
-Mike Tyers (Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto).... read more

Posted by Scott Cain 2005-09-12

Fall, 2005 GMOD workshop announcement

Hello,

After much wrangling with the Meetings people at CSHL, I am pleased to
announce that the Fall GMOD Workshop will take place at Cold Spring
Harbor Lab on October 27 and 28, which is immediately prior to the
Genome Informatics meeting, also at CSHL.

Register here:

http://www.gmod.org/register.shtml

This workshop will be somewhat different from previous GMOD meetings, as
there will be no "show and tell" and its focus will be on what can be
done and what should be done to make the 'core' GMOD tools work together
in a seamless way. These tools are:... read more

Posted by Scott Cain 2005-08-25

BioMart relaunched as a collaboration with Cold Spring Har

We are pleased to announce that BioMart is now a collaborative project
between European Bioinformatics Institute and Cold Spring Harbor Laboratory.
We are confident that building on the experience and strength of the institutions
that are key players in the field of bioinformatics will help us to further improve
our software.

The new BioMart website is now available at http://www.biomart.org

On behalf of the BioMart team,
Arek Kasprzyk... read more

Posted by Scott Cain 2005-08-25

Flash GViewer tool released

I've put a Macromedia Flash version of the RGD GViewer tool into the
GMOD repository and it is now available for download from the
sourceforge site (http://sourceforge.net/projects/gmod). It requires
the Flash plugin (Version 7) to run (if you just have version 6 it
opens but doesnt load any data).

GViewer is a web-based genome visualization tool that shows an
organism's chromosomes (and banding patterns which could be the usual
p and q cytogenetic bands or syntenic regions or feature density -
whatever you want to show) and features which align with the
chromosomes such as genes, QTLs, probesets, etc. It is intended to
provide an overview of the locations of targetted sets of features -
proteins identified in a proteomics experiment, genes differentially
regulated in a microarray experiment, genes and QTLs associated with
a phenotype, etc. The features can hyperlink out to a report page,
you can zoom in an view single chromosomes with the features laid out
and labelled for easier viewing, etc.... read more

Posted by Scott Cain 2005-08-20

First International Biocurator Meeting, Asilomar, CA, Dece

** First announcement **
First International Biocurator Meeting, Asilomar, CA, December 8-11, 2005

The goal of this meeting is to create a forum for curators and developers of
biological databases to discuss their work, promote collaborations, and foster
a sense of community in this very active and growing area of research.
Confirmed plenary speakers include Rolf Apweiler (EBI), Russ Altman (Stanford
University), and Mike Tyers (University of Toronto).... read more

Posted by Scott Cain 2005-08-20

Final alpha release of gmod (chado)

Hello,

I am pleased to announce that the last alpha of the GMOD core schema,
chado, and its associated tools has been released. It can be downloaded
from:

http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=19511

There have been many changes in this release, including a smoother build
procedure, a bulk GFF3 loader that is much faster than the Class::DBI
based loader (though the Class::DBI loader is still included and
supported), and sample code for making Apollo read and write to chado.
There is much to do for the first 'real' release of gmod/chado. From
the TODO file:... read more

Posted by Scott Cain 2005-07-08

SynBrowse newly released

Hello,

This is to announce that SynBrowse has been released.

SynBrowse (Synteny Browser) is a generic sequence comparison tool for
visualizing genome alignments both within and between species. It is intended
to help scientists study and analyze synteny, homologous genes and other
conserved elements between sequences. This software is useful in studying
genome duplication and evolution. It can also aid in identifying
uncharacterized genes, putative regulatory elements and novel structural
features of study species by comparing to a well annotated reference sequence,
thus enabling genome curators to refine and edit annotations of species that
have incomplete genome annotations. ... read more

Posted by Scott Cain 2005-06-30

GMOD demos at ISMB

Hello,

There are several GMOD-related demos at the ISMB meeting; if you are in
at the meeting, please feel come by and show your support and ask your
questions. The demos are:

SynBrowse: A Synteny Browser for Comparative Sequence Analysis
Sunday, June 26 - 9:30-10:30am, room: Nicolet
Author(s): Xiaokang Pan, et. al.
Short Description: We have developed SynBrowse, a synteny browser for
visualizing and analyzing microsynteny, macrosynteny, homologous genes
both within and between species. SynBrowse is a GBrowse family software
tool that runs on top of the open source Bioperl modules. It consists of
two components: a web-based front end and a set of relational database
back ends. Each database stores pre-computed comparative alignments from
a focus sequence to reference sequences and genome annotations of the
focus sequence. The user interface lets end users search for syntenic
blocks between two sequences and zoom in to view the detailed
comparisons.... read more

Posted by Scott Cain 2005-06-22

BioMart version 0.3 released

We are pleased to announce the release of BioMart version 0.3

The new BioMart release comes with support for three RDBMS platforms:
MySQL, Oracle and Postgres. Additionally, BioMart works with
the following third party software: Bioconductor package biomaRt,
Taverna workflow system and DAS ProServer.

The overall configurability of the system has been greatly improved.
It is now possible to run different dataset versions within the same
BioMart instance and have a customised remote dataset retrieval.
MartView has more configuration options and supports more filter
types. MartEditor comes with many usability improvements and
configuration validation preventing run time problems.... read more

Posted by Scott Cain 2005-06-17

CSHL Genome Informatics Meeting

Hello,

The Cold Spring Harbor Laboratory Genome Informatics meeting is this fall,
October 28 to November 1, 2005. The Abstract deadline is August 3, 2005.
For more information see the CSHL website at

http://www.cshl.edu/meetings/info05.shtml

or this pdf on the GMOD website:

http://www.gmod.org/info05.pdf

Thanks,
Scott

----------------------------------------------------------------------
Scott Cain, Ph. D. cain@cshl.org
GMOD Coordinator, http://www.gmod.org/ (216)392-3087
----------------------------------------------------------------------... read more

Posted by Scott Cain 2005-06-10

Presentations from GMOD meeting online

Hello,

I am pleased to announce that the presentations from last weeks GMOD
meeting are now online at:

http://www.gmod.org/workshops/2005/may/

Please let me know if you have any questions or problems.

Thanks for a great meeting,
Scott

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Posted by Scott Cain 2005-05-25

Architecture working group - call for participation

Hello everyone,

At the GMOD meeting in Menlo Park earlier this week, the decision was made
to form an architecture working group for GMOD. The working group will
propose, discuss, investigate, and finally recommend architecture decisions
to the rest of the GMOD group. The hope is that a common set of
architectures will lead to a more integrated project with efficient code
reuse. My name is Eric Just and I volunteered to be the coordinator of
this group. I would like to extend an invitation to everyone who is
interested to participate. Initially we will use the gmod-devel list at
sourceforge ( http://lists.sourceforge.net/lists/listinfo/gmod-devel ) as
our discussion platform. I would like to have representatives from each
Model Organism Database so please forward this message to as many people as
you want who may not be on the gmod-devel list yet.... read more

Posted by Scott Cain 2005-05-20

GMOD meeting agenda

Hello,

Below is the agenda for the May 16-17 GMOD meeting. Please let me know
if you have any comments. If you are presenting, please send me a copy
of your presentation so I can put it on the GMOD website.

Thanks,
Scott

Monday Morning

9:00 introductions--Scott Cain
9:15 misc updates (gbrowse, SGD, pub*, others?)

10:00 coffee

10:15 my trip to france (setting up ParameciumDB)
Scott Cain
10:45 Textpresso update
Eimear Kenney
11:15 Pathway Tools Update
Peter Karp... read more

Posted by Scott Cain 2005-05-12

gmod-0.003 release candidate 2

Hello,

I am pleased to announce the availability of gmod alpha version 0.003
release candidate 2:

http://brebiou.cshl.edu/gmod/gmod-0.003-RC2.tar.bz2

If you don't remember the first release candidate, I don't blame you, it
was quite some time ago.

This release brings with it the most current chado schema and a greatly
enhanced GFF3 loading tool, gmod_bulk_load_gff3.pl, which should be able
to handle nearly all GFF3 loading needs (and it does not rely on
Class::DBI): it can now load reference/srcfeatures, it can load DNA
sequences and analysis results.... read more

Posted by Scott Cain 2005-05-10

rough draft agenda for GMOD meeting

Hello,

Below is a rough draft of the meeting agenda for the GMOD meeting being
held at SRI on May 16-17. Please go to

http://bioinformatics.ai.sri.com/gmod05/

for more registration and lodging information on the meeting.

Note that this agenda is a rough draft, and the talk 'titles' are only
typically only placeholders until I get a real title, but hopefully the
subject matter will match up. Please let me know if:... read more

Posted by Scott Cain 2005-04-25

Hackathon 2005

(sorry for multiple postings, but please do forward to
anyone else who you think might be interested)

------------------------------------------------------------------------
-----------

Dear everyone,

It has been a long time and we Bioinformatics devotees are overdue for
another total-immersion coding-fest (the last hackathon was held in
Singapore February 2003, more than two years ago). Apple has offered
to host us this year, and as an added bonus include free admission to
the World-Wide Developers Conference in San Francisco the prior week.
They are also looking for some people to present interesting new
developments at the WWDC, so if you have something noteworthy please
let us know. Apple is not attaching any strings, so our work need not
address Apple-specific software or hardware areas. Apple will provide
space and hardware (and access to their engineers if we'd like).... read more

Posted by Scott Cain 2005-04-20

Registration and hotel info for GMOD meeting

Hello,

Please see the following page for registration and hotel information for
the GMOD meeting on May 16-17 at SRI in Menlo Park:

http://bioinformatics.ai.sri.com/gmod05/

A tentative agenda will available later today or tomorrow.

Thanks,
Scott

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Posted by Scott Cain 2005-04-18