[Gmod-help] Re: [Wg-emod] starting up with gmod...

[GMOD Help Desk]

Hello Mark,

Responses to some of your questions are below.  I have CC'd this
message to the GBrowse and CMap e-mail lists because there are people
on those lists who can probably answer the other questions.

Dave Clements
GMOD Help Desk

On Oct 30, 2007 7:08 AM, Mark Mandel <mandel01 at gmail.com> wrote:
> Hello Helpdesk,
>
> I am working on building a "model organism" resource for Vibrio fischeri and
> the GMOD resources seem very appealing.  I am writing because I found your
> "GMOD for the Biologist" page in your Wiki and that fits me very well, so I
> wanted some feedback before I get started.
>
> My goals are to have an easily searchable interface for the V. fischeri
> ES114 genome (which we have recently resequenced and reannotated), which it
> seems that gbrowse will accomplish very well!  Looking toward the future,
> there are additional features that will be particularly valuable:
>
> 1. links to papers that are related to the genes involved (we have a curated
> list of Pubmed ID's at this point but will want to add to it).
> 2. user-added gene annotations or information as gene names and annotations
> change.
> 3. comparative genomics with other bacterial strains of this species, since
> others are in the pipeline to be sequenced.  I saw the cmap page but wasn't
> sure if this was well-adaptable to bacterial genomes.

GBrowse is indeed the tool you want for displaying the sequence and
the annotation.  How are you currently making and recording your
annotations?  Apollo is another GMOD component that might be able to
help with that.

I am not sure if GBrowse can link to papers.  This may require GBrowse
to run on Chado.  Can someone on the GBrowse list address this
question?

GMOD components are widely used with bacteria.  I do not know if CMap
is in use with bacterial maps or not.  Ben (or anyone else on the CMap
list), do you know of any sites using CMap with bacteria?

> I am going to start installing the basic gbrowse w/gff annotations and see
> how it goes, but if you had any other comments (or knew of other examples of
> smaller bacterial comparative genomics/annotation projects) that would be
> appreciated.

See http://gmod.org/wiki/index.php/GMOD_Users for a partial list of
sites that use GMOD components.  That page also lists GBrowse users at
the end.  Unfortunately this list is several years old and without
links.

> In general most of my database work has been in Microsoft Access (I use
> Windows), and I have a rudimentary Python and Perl knowledge that I am
> working on enhancing.  But I am principally a *biologist* and most
> importantly want to build a system that will be easy to maintain and keep
> up-to-date, not one that is always waiting for me to learn some more
> programming!!

With GBrowse, you almost certainly won't have to do significant (or
maybe even any) Perl coding.  You will need to know how to install
things.  Windows is a supported platform, but it is probably the least
used platform in the GMOD world.  Questions that are Windows specific
will have a smaller pool of people that are able to respond.

> Thanks in advance for any comments.
>
> Regards,
> Mark Mandel
>
> mandel01 at gmail.com
> http://www.vfdna.org/
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