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

[Mark Mandel]

Thanks Dave!

On 10/30/07, GMOD Help Desk <help at gmod.org> wrote:
>
> 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/
> > _______________________________________________
> > Wg-emod mailing list
> > Wg-emod at nescent.org
> > https://lists.nescent.org/mailman/listinfo/wg-emod
> >
> >
>
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