[Gmod-help] cosmoss.org Physcomitrella mod

[Daniel Lang]

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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

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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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