[Gmod-help] Re: Amborella Genome

[Jim Leebens-Mack]

Hi Dave,

I will try calling you Friday morning or early afternoon your time.  Let me know if you have a preference.

Bests,
Jim 


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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
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----- Original Message -----
From: GMOD Help Desk
[mailto:gmodhelp at googlemail.com]
To: Jim Leebens-Mack
[mailto:jleebensmack at plantbio.uga.edu]
Cc: GMOD Help Desk
[mailto:help at gmod.org]
Sent: Thu, 20 Dec 2007 13:30:29 -0500
Subject: Re:
[Gmod-help] Re: Amborella Genome


> 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>
> > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >
> >
> >
>