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/MolgenisCore - core platform of model parsers, generators, framework and utils
 * wiki:Plugins/MolgenisDatabase - database interface framework on top of MySQL, PostgreSQL and HypersonicSQL
 * wiki:Plugins/MolgenisUi - user interface framework that can be run on the internet
 * wiki:Plugins/MolgenisAuth - authentication and secure sharing framework
 * wiki:Plugins/MolgenisProcessing - for easy modeling and running of analysis tools

= Data oriented plugins = 
 * wiki:Plugins
 * wiki:Plugins/DataMatrix - 
 * wiki:Plugins/MolgenisPheno -
 * wiki:Plugins/Mutations - for representing and working with mutations
 * [Modules/XGAP Molecular Phenotypes]
 * [Modules/OntoCAT Ontologies]

= Systems =
Systems are ready to use and download:
 * [Systems/XGAP GWAS studies]
 * [Systems/XGAP QTL studies]
 * [Modules/S Sequence LIMS]
 * [Modules/XGAP Animal Observatory]
 *