[Gmod-help] Re: Amborella Genome

[Vision, Todd (Biology)]

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