MOLGENIS by example: generating an extensible platform (ISMB DAM/BOSC 2009)

…for genotype and phenotype experiments

Morris Swertz, Groningen

MOLGENIS is a database generator – a free toolbox of automated best practices and more. We separate out the parts that are different from the parts that are common in their applications. The blueprint is written in XML and then templates are written which translate that XML into working software. The first step in MOLGENIS is modelling (though you can also extract a model from an existing database that isn’t yet part of MOLGENIS). Then a set of generators are run that will build the appropriate apps. The generators are implemented in Freemarker. The programmer can the build on the generated code if they like.

He spent some of the time on a demo of MOLGENIS itself.

XGAP (Xtensible Geontype and Phenotype data platform) – DAM challenges include sharing data between QTL collaborators, variety of species and methods, ensure there is reuse of ad-hoc analysis protocols. XGAP extends the FuGE standard. Their project plus 6 others are described in XGAP format.

The next step is to add  more semantics into it. They would also like to do some federation and cloud computing.

FriendFeed discussion: http://ff.im/4vnGO

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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