[Gmod-help] Re: Amborella Genome

[GMOD Help Desk]

Hi Jim,

My phone number is 541 914 6324.  I'd be happy to talk to you about getting
started with GMOD.  I'm available today (Thursday), all day or tomorrow
(Friday) from noon Eastern on.  (I'm on the west coast.)  I'm also available
next Thursday and Friday.

Some pointers:
*Physical Maps:* See CMap, http://gmod.org/CMap
*Genome Viewer:* See GBrowse, http://gmod.org/GBrowse
*Synteny*: This choice is less clear.  See http://gmod.org/Synteny.  I am
currently trying to figure out the status of each of these choices.  The
owner of SynBrowse, for example, isn't answering e-mail these days.  Look
for that list to be updated in the next month or so.
*Data Management*: Chado is a good way to manage your data.  You can run
some of the above tools directly on Chado, or you can export data from Chado
and run them on the exported data.  See http://gmod.org/Chado.

I'd also take a look at http://gmod.org/Computing_Requirements.  This will
give you an idea of what sort of personnel and hardware you will need to
support a GMOD installation.

Please let me know if you have any questions.

Thanks,

Dave Clements
GMOD Help Desk

On Dec 20, 2007 7:18 AM, Vision, Todd (Biology) <tjv at bio.unc.edu> wrote:

> Hi Jim,
>
> I'm headed off for the holidays tomorrow and won't be back till Jan 3rd or
> so.  But Dave Clements, who staffs the GMOD help desk now, is prepared to
> give you exactly this kind of assistance. Dave has also done wonders with
> the documentation available at www.gmod.org.  I know he was working on a
> user story for ParameciumDB, which is a very small lab that has recently
> made their database and website entirely from scratch using GMOD tools.
>  You
> might want to ask him about that.  I have copied Dave on this email
> (through
> the help at gmod.org address).
>
> Also, Scott Cain will be giving a Gbrowse tutorial at PAG  I sat in on it
> last year, and I highly recommend it.
>
> Yes, we are putting a Gbrowse instance up on mimulusevolution.org right
> now,
> and it is turning out to be easier than we had anticipated.  That said, it
> still takes a dedicated informatics person to maintain Chado-Gbrowse-CMap
> if
> the data keeps changing -- it's not something I would recommend you try to
> do in your spare time!
>
> We should talk about the synteny and gene family viewers when I get back
> in
> January, as there might be some synergy there.
>
> Cheers,
> Todd
>
>
> On 12/20/07 9:13 AM, "Jim Leebens-Mack" <jleebensmack at plantbio.uga.edu>
> wrote:
>
> > Hi Todd,
> >
> > Claude, myself and others will be submitting a PGRP proposal to sequence
> large
> > portions of the Amborella genome in order to better understand the
> evolution
> > of genome structure throughout angiosperm history.  If funded we would
> extend
> > our current physical map for the Amborella genome and then sequence
> ~1000 BAC
> > pools covering 1-2 MB contigs.  We would use GMOD to develop an
> Amborella
> > genome browser with track for other plant sequences and links to a
> syntenic
> > block viewer and gene family phylogenies.
> >
> > I suspect you are doing the same with the Mimulus genome.  I wonder if I
> could
> > pick your brain about the best methods for launching a new GMOD project.
>  Let
> > me know if you have time for a phone call some time over the next few
> days.
> >
> > Bests,
> > Jim
> >
> >
> >
> >
> > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> > Jim Leebens-Mack
> > Department of Plant Biology
> > University of Georgia
> > Athens, GA 30602-7271
> >
> > Phone: 706-583-5573
> > Fax: 706-542-1805
> > email: jleebensmack at plantbio.uga.edu
> > url: http://www.plantbio.uga.edu/~jleebensmack/JLMmain.html<http://www.plantbio.uga.edu/%7Ejleebensmack/JLMmain.html>
> > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
>
>
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