[Gmod-help] chado for bacterial genomes

[Scott Cain]

Hi Victor,

Just to follow on a little bit: the web front end that we use in GMOD is
a tool based on Turnkey, a perl/Class::DBI tool.  However, it is still
somewhat immature and a little difficult to install.  It is currently in
use by ParameciumDB though (http://paramecium.cgm.cnrs-gif.fr/ ).
Another option being worked on by someone in our group is a Drupal-based
front end which has the potential of doing as much as Django.  Drupal is
php based and has a fairly large community of users and developers.

Scott

On Wed, 2008-01-16 at 15:56 -0800, Dave Clements, GMOD Help Desk wrote:
> Hi Victor,
> 
> I've cross-posted my response to the GMOD Schema list, which is about
> Chado.  People may have some additional comments.
> 
> There are a number of bacterial projects using GMOD.  Here are some:
> 
> EcoliWiki: http://ecoliwiki.net/  EcoliWiki uses GMOD components
> including GBrowse and TableEdit.   Jim Hu <jimhu at tamu.edu>.  
> Pathema: http://pathema.tigr.org/Burkholderia/beta/  Pathema uses
> Chado.
> GeneDB: http://www.genedb.org/  GeneDB also uses Chado.
> 
> Take a look at http://gmod.org/GMOD_Users for more. There may be
> others on the mailing list who may also respond to your question.
> 
> To answer your second question, as far as I know, there are no Python
> based software tools in GMOD.  We are mainly a Perl organization with
> some prominent Java components.  However, to use GMOD you shouldn't
> have to do much if any Perl programming.  You will, however, have to
> understand how to do Perl installs. 
> 
> Please let me know if you have any questions,
> 
> Dave C
> GMOD Help Desk
> 
> On Jan 16, 2008 8:08 AM, Victor de Jager <victor.dejager at gmail.com>
> wrote:
> > Hi there,
> > 
> > I'm looking into options for using the chado scheme to build a
> > bacterial genome annotation database with experimental evidence
> based
> > annotations.
> > I would like to know if there are groups who use the chado scheme
> and 
> > gmod tools for bacterial genomics. If so, who might I contact?
> > 
> > As a second question, are you aware of any python based software
> tools
> > for the chado database (Using Django models maybe?). I am basically
> a 
> > python programmer so perl would mean an extra effort in learning.
> > 
> > best regards
> > 
> > Vic de Jager
> > 
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory