[Gmod-help] Re: [apollo] Who is using the Apollo?

[James Estill]

Hi all --

We are using Apollo for a number of projects here at the University of Georgia (UGA) involving gene and transposable annotation in plant genomes. These projects have included strawberry, maize, tetraploid wheat, and diploid wheat.  We have found Apollo to be a great interface for annotating genes, but like all other annotation curation solutions it is not as strong at representing the complicated biology that TEs can have. Our 'DAWGPAWS' annotation suite (http://www.plantmethods.com/content/5/1/8) concatenates computational results that we curate in Apollo, and I have been working a bit with the author of the TriAnont pipeline (http://urgi.versailles.inra.fr/projects/TriAnnot/) to make the TriAnnot annotation results compatible with Apollo as well. We have generally not used Apollo with a Chado DB, and have mostly relied on game.xml files to store and communicate our annotation results. Apollo was also used in a wheat genome annotation training workshop in Baltimore (announcement at http://news.gramene.org/?p=206) that I was recently involved in.

Also, FYI the DAWGPAWS subversion repository contains some emacs modes that I find useful when editing tiers/types files (http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/trunk/emacs_modes/). I'm no emacs expert, but I have found these helpful since I often like to spell things wrong when hastily writing config files.

-- Jamie Estill
-- jestill at uga.edu
-- http://jestill.myweb.uga.edu
-- http://www.epernicus.com/people/jestill


----- Original Message -----
From: Ed Lee
[mailto:elee at berkeleybop.org]
To: Scott Cain
[mailto:scott at scottcain.net]
Cc: apollo at fruitfly.org, Dave Clements, GMOD
Help Desk [mailto:help at gmod.org]
Sent: Fri, 02 Oct 2009 16:11:22
-0400
Subject: Re: [apollo] Who is using the Apollo?


> Hi Daniel,
> 
> We did an informal survey of the user base about a year ago and to
> add Scott's list:
> 
> * Howard Hughes Medical Institute SEA
> * UGA
> * Nasonia
> * VectorBase
> * Ensembl GeneBuild
> * Hamilton College
> 
> There are some other groups that have shown interest in starting to
> use Apollo, although I'm not sure whether or not they have done so.
> 
> Cheers,
> Ed
> 
> On Fri, 2 Oct 2009, Scott Cain wrote:
> 
> > Hi Daniel,
> >
> > At a GMOD meeting a few years ago, the participants came up with a list of
> 
> > groups that we knew of that were using Apollo with Chado (there are
> probably 
> > other users, but we weren't interested in the for that list).  The ones we
> 
> > came up with are here:
> >
> > http://gmod.org/wiki/Apollo#Users
> >
> > Scott
> >
> > On Oct 2, 2009, at 3:19 PM, Dave Clements, GMOD Help Desk wrote:
> >
> >> Hi Daniel,
> >> 
> >> As far as I know, there is not a list of Apollo users anywhere.
> >> People don't have to register to download and use it.  Creating a list
> >> of GMOD users and what components they use is on my todo list, but I
> >> don't know when I'll get to it.
> >> 
> >> In the meantime, the best way to find out who is using it, may be to
> >> look at the archives for this list.  Go to
> >> http://mail.fruitfly.org/mailman/private/apollo/.  You'll need your
> >> email address and list password (which was mailed to you when you
> >> joined the list.).
> >> 
> >> Dave C.
> >> 
> >> On Fri, Oct 2, 2009 at 6:50 AM, Daniel Xavier de Sousa
> >> <danielucg at yahoo.com.br> wrote:
> >>> Hello,
> >>> 
> >>> I`m quite new here, and a would like to know who is using the Apollo
> now?
> >>> 
> >>> I`m looking for a web system to run a medium genome project. I hope to
> >>> process the pipeline: calling sequences, cleaning the vector, clustering
> 
> >>> and
> >>> annotation.
> >>> 
> >>> Thanks for all,
> >>> 
> >>> 
> >>> -Daniel Xavier de Sousa
> >>> 
> >>> ________________________________
> >>> Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 -
> >>> Celebridades - Música - Esportes
> >>> _______________________________________________
> >>> apollo mailing list
> >>> apollo at fruitfly.org
> >>> http://mail.fruitfly.org/mailman/listinfo/apollo
> >>> 
> >>> 
> >> 
> >> 
> >> 
> >> -- 
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> >> http://mail.fruitfly.org/mailman/listinfo/apollo
> >
> > -----------------------------------------------------------------------
> > Scott Cain, Ph. D. scott at scottcain dot net
> > GMOD Coordinator (http://gmod.org/) 216-392-3087
> > Ontario Institute for Cancer Research
> >
> >
> >
> >
> > _______________________________________________
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> > apollo at fruitfly.org
> > http://mail.fruitfly.org/mailman/listinfo/apollo
> >