[Gmod-help] chado for bacterial genomes

[Victor de Jager]

Hi Scott and Dave,

thanks for your replies. I will contact Jim Hu and the genedb people
as these projects seem to resemble what we want to achieve in time. In
between I have been successful to get the schema into Postgresql. I
haven't looked at all the tools yet, but hope to do so next week (i'm
working only a few hours a week on this project)

Victor



On Jan 17, 2008 1:08 AM, Scott Cain <cain.cshl at gmail.com> wrote:
> 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
>
>