[Gmod-help] cosmoss.org Physcomitrella mod

[Scott Cain]

Hi Daniel,

Yes, I remember talking to you, and you probably talked with Dave
Clements as well.

Have you talked to the Apollo folks (Ed Lee and Suzi Lewis) about your
work?  That would be the most sensible thing to do.  The good news
that I just recently heard (second hand, so I hope it's true), is that
they just received some funding for continued development on Apollo.
In my mind, that would make now a good time to approach them with
these ideas/contributions.

I have one question (to start with :-) about what you described below:
do you really have a way to have Apollo talk to a
Bio::DB::SeqFeature::Store database?  That is interesting indeed,
since it stores serialized perl objects.  You must be deserializing
them in perl and then having Apollo talk to that?  Or is Apollo
talking to a web service that is using the perl adaptor?  And what
about writing back?  (OK, that morphed into multiple questions!)

Here are Ed's and Suzi's contact info:
Ed: elee at berkeleybop.org
Suzi: suzi at berkeleybop.org

Scott


On Thu, Apr 15, 2010 at 4:52 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.
>
> 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.
>
> 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.
>
> 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.
>
> 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:-)
>
> 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:     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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-- 
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research