[Gmod-help] Getting started GMOD

[Dave Clements, GMOD Help Desk]

Hi Scooter,

On Mon, Sep 14, 2009 at 12:21 PM, Scooter Willis <HWillis at scripps.edu> wrote:
> I wanted to see if I can get some initial feedback on the following
> questions as we are about to do a GMOD install for a newly sequenced genome.
>
>
> 1. Is it possible to download the VMWare instance that was built at the last
> GMOD meeting?

The VMware images for both courses are available at:
ftp://ftp.gmod.org/pub/gmod/Courses/2009/

> 2. What are the tradeoffs on going with Chado or BioSQL for the database? I
> don’t see the need for any customizations in our current project so want to
> keep it simple and be in the best position to use Gmod and other add on
> tools. We will be wanting to do some level of BLAST search integration and
> Comparative Genome with GBrowse_syn if that makes a difference for Chado or
> BioSQL.

I usually tell people to use SeqFeature::Store to back their GBrowse
instance, if at all possible.  It's faster than other choices, and
much faster than Chado.  It does require you to periodically dump your
chado database in GFF3 and reload it into MySQL.

I can't address the strengths and weaknesses of BioSQL, as I don't
have experience with it.  People use Chado if they don't care so much
about speed, or if they want to see their data immediately after
updating / loading it in Chado.  Chado also supports recursive feature
localization:  In Chado, everything does not have to directly map to
the reference chrom/contig.  In SeqFeature::Store everything is placed
directly on the chromosome.

> 3. In looking at the Installing Chado and Ubunto Howto page  it looks like
> postgre is mentioned. Our preference is mysql but could also do postgre.
> What is the recommendation and/or what are the developers/end users
> typically use?

For Chado, the overwhelming choice is Postgres.  You will have to do
the least amount of conversion if you use Postgres.  (See
http://gmod.org/extras/2008GMODCommunitySurvey.html#Chado)

> 4. Do I need a specific version of Ubunto 32bit or 64 bit?

I don't know.  When I install stuff I always use a 32 bit version of
Ubuntu, just because I have had too much trouble with 64 bit libraries
not existing.  That preference may not reflect current reality though.

Hope this helps,

Dave C.

> Thanks
>
> Scooter Willis



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