[Gmod-help] re: EST database

[Dave Clements]

Dear Leo,

Preparation for the Chado Workshop would certainly help, but none is
absolutely necessary.  Good places to start include:

http://gmod.org/wiki/index.php/Introduction_to_Chado
  Explains how sequence based features, such sequences and ESTs, are
represented in Chado.
http://gmod.org/wiki/index.php/Image:A_Chado_Case_Study.pdf
  The official publication describing Chado.
http://gmod.org/wiki/index.php/Chado_Manual
  Explains Chado architecture from a computing point of view.

Data in a Chado database can be made available online in a couple of
ways.  GBrowse will be able to display your sequence based data, and
if most of what you have is sequence based data then GBrowse might be
able to meet all your display needs.  See
http://gmod.org/wiki/index.php/GBrowse.

To answer your other question, I would say that GMOD tools require
someone in your organization who has at least moderate computer
skills.  In particular, they will need experience with Linux system
administration and a scripting language (Perl, Python, etc) to
successfully use Chado for your needs.  See
http://gmod.org/wiki/index.php/Computing_Requirements for more.

Finally, if GMOD looks like it can meet your needs, you should
consider sending someone to the 2008 GMOD Summer School.  See
http://gmod.org/wiki/index.php/GMOD_Summer_School.

Please let me know if you have any questions or comments,

Dave Clements,
GMOD Help Desk

On Mon, Mar 10, 2008 at 11:17 AM, L Saldivar <leo.saldivar at ars.usda.gov> wrote:
> Greetings GMOD folks,
>
>  Our lab works with agricultural pests, e.g. ticks, flies.   We have been
>  accumulating genomic data, mainly EST libraries for some years now.
>
>  We would love to have a database in which to put all our data into and be
>  able to run translations, have BLAST, GO and PIR annotation, etc.  We would
>  also want to have it online.  We currently do not have a database, unless
>  you call fasta files and Excel workbooks a database.
>
>  We want to have a way of updating the database and that is not heavy on
>  computing skills.  Are these strengths of GMOD?
>
>  I will be attending your Chado workshop on Aprill 11.  Do you have any
>  suggestions on how I can get started so as to better benefit from the
>  workshop?
>
>
>  thanks,
>
>  Leo
>
>
>
>  --
>  Leonel (Leo) Saldivar
>  Bioinformatician
>  USDA-ARS
>  Knipling-Bushland U.S. Livestock
>   Insects Research Laboratory
>  2700 Fredericksburg Rd.
>  Kerrville, TX 78028
>  830.792.0366
>  830.792.0314 (Fax)
>  Leo.Saldivar at ars.usda.gov
>
>
>