[Gmod-schema] [Gmod-help] chado for bacterial genomes

[Jim Hu]

Hi Victor,

We're just starting to work on getting E. coli information into  
Chado.  It may be good to share our experiences as we go along.  I  
believe that TIGR has done a bit with Chado and bacteria as well.

Jim

On Jan 23, 2008, at 5:59 AM, Victor de Jager wrote:

> 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
>>
>>
>
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=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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