[Gmod-help] cosmoss.org Physcomitrella mod

[Dave Clements]

Hi Daniel,

I'm going to add some to what Scott said and address some other areas as
well.

On Thu, Apr 15, 2010 at 1:52 AM, Daniel Lang <
daniel.lang at biologie.uni-freiburg.de> wrote:

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> Hi,
>
> we are currently writing a grant (German Science Foundation) to
> establish a mod for the genome of the moss Physcomitrella patens.
> Community-wise ours is small but growing: around 500 people worldwide
> are working with the moss or are using it as an additional plant model.
>

500 people is actually a fairly large community compared to many that use
GMOD.  Some are less than 5 labs.

cosmoss.org has been online since 2003 and offers basically BLAST and
> gbrowse access to bryophyte genomics and transcriptomics data. We have
> and are now extending our services to enable community annotation: we
> have an online GOA tool and are extending Apollo to interact directly
> Bio::DB::Seqfeature.
>

Suzi Lewis confirmed that the new Apollo grant has been definitively funded
and that work start on 1 May.  (Now you've heard it second and third hand.
:-) I also urge you to contact Ed and Suzi.

We have been using GMOD components for years now and want to use this
> opportunity to give something back and contribute to GMOD.
>
> Our project plan includes the creation of a standalone, CHADO-based Java
> webstart app, that allows ontology annotation of a set of genes.
> Basically a generic OA editor that would be able to write back to CHADO
> and a GOA-like plain text format.
>
> Furthermore we are migrating our annotation backends to CHADO and will
> develop an Expression Atlas module (like the EMBL Gene Expression Atlas;
> Kapushesky et al 2009; NAR) and a Interaction data module. Both will be
> ontology based making as much use of existing OBO ontologies as
> possible. The tools itself will be visualizers and mining tools running
> on CHADO infrastructure. From these efforts either only the SQL
> extensions or the perl-based software or both could be contributed to GMOD.
>

Patrick Leamaire's group in Marseilles (Patrick <lemaire at ibdml.univ-mrs.fr>,
ANISEED Group <aniseed at ibdm.univ-mrs.fr>), is fairly far along in porting
the NISEED platform to use Chado.  That will include a web front end for
viewing and curation.  NISEED supports atlases for expression, phenotypes
and cell fates.  Patrick is also very interested in interaction networks.  I
strongly urge you to contact Patrick to let find out if what his group is
doing will work for you.  I'm hoping to make the NISEED platform a part of
GMOD.

GMOD does not (in my opinion) have an integrated solution for interaction
data.  We do have Pathway Tools (http://gmod.org/wiki/Pathway_Tools) which
covers this.  It has many GMOD users, but it does not integrate with
anything else in GMOD.  It is also not open source.  There's also been talk
of bringing NBrowse (http://gmod.org/wiki/NBrowse) into GMOD, but we have no
definitive plans.  Anything that would help us in this area would help us.


> If there is interest, we would gladly commit our Apollo extensions as
> well...
>
> For our proposal to be successful, it would be crucial for us to know
> what you think of these ideas and if you would support us. As always,
> the deadline is close - the end of April.
>
> What we could offer would be 3 dedicated developers for at least 3-6 years.
>

That's absolutely great.  This is one of our requirements that people often
don't think about.  See http://gmod.org/wiki/GMOD_Membership for what is
needed to become a part of GMOD.

>
> I think we might have met in person at last years GMOD meeting after the
> PAG -  I was there with my colleague Andreas Zimmer.
>
> Thank you for reading this far:-)
>

Likewise!

Dave C


> Looking forward to hearing from you.
>
> All the best,
> Daniel
> - --
> Dr. Daniel Lang
> University of Freiburg, Plant Biotechnology
> Schaenzlestr. 1, D-79104 Freiburg
> fax:        +49 761 203 6945
> phone:      +49 761 203 6989
> homepage:   http://www.plant-biotech.net/
>            http://www.cosmoss.org/
> e-mail <http://www.cosmoss.org/%0Ae-mail>:
> daniel.lang at biologie.uni-freiburg.de
>
> #################################################################
> Explore the moss genome
> at the 3rd cosmoss.org Physcomitrella Genome Workshop from
> September 13th-15th 2010 in Freiburg
> https://www.cosmoss.org/physcome_project/wiki/Cosmoss_workshop
> ################################################################
>
>
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