[Gmod-help] chado for bacterial genomes

[Dave Clements, GMOD Help Desk]

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
>
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