Status: this is under development for MOLGENIS 4.0
Don't expect this if you use MOLGENIS 3.x!

MOLGENIS is organized as a set of modules which we call plugins. Each plugin adds a combination of MolgenisModels, MolgenisDomainSpecificLanguage, MolgenisGenerators and/or handwritten code. Other plugins may extend other plugins to yet add more functionality. The first plugin where all others build upon is the MOLGENIS database core. The last plugin is typically a fully functional application that assembles other plugins 

TODO core architectural picture.

= Software oriented plugins =
 * wiki:Plugins/OrgMolgenisCore - core platform of model parsers, generators, framework and utils
 * wiki:Plugins/OrgMolgenisDb - database interface framework on top of MySQL, PostgreSQL and HypersonicSQL (extends core)
 * wiki:Plugins/OrgMolgenisUi - user interface framework that can be run on the internet (extends db)
 * wiki:Plugins/OrgMolgenisAuth - authentication and secure sharing framework (extends db, ui)
 * wiki:Plugins/OrgMolgenisProcessing - for easy modeling, integration and running of analysis tools (extends ui, db, core) 

= Data oriented plugins = 
 * wiki:Plugins/MatrixData -  
 * wiki:Plugins/PhenoData -
 * wiki:Plugins/MutationData - for representing and working with mutations

= Systems =
Systems are ready to use and download:

In the wet lab:
 * wiki:Plugins/

Repositories:
 * wiki:Plugins/ShortReadMolgenis - for storing short read data

Downstream:
 * wiki:Plugins/GwasMolgenis - for GWAS studies like in EU-GEN2PHN, LifeLines and BBMRI-NL
 * wiki:Plugins/QtlMolgenis - for QTL studies in model organisms like EU-Panacea
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