[[TOC(depth=2,MolgenisIntro,MolgenisOnWindows,MolgenisOnUbuntu,MolgenisOnEclipse,MolgenisWorkspaceBasics,MolgenisGeneratorBasics,MolgenisAddressBookExample,MolgenisFromExisting,MolgenisLanguageReference,MolgenisDtd,MolgenisPlugin,MolgenisDatabase,MolgenisEmail,MolgenisBatchLoading,MolgenisRinterface,MolgenisSoapInterface)]]

= The MOLGENIS user guide =
This MolgenisGuide is meant to serve as a starting point for all documentation regarding MOLGENIS usage for application development. The guide is a free document, a collaborative effort, and a part of the  MOLGENIS Project itself.

== Table of Contents ==
Available documentation:

 * MolgenisIntro -- Introduction into MOLGENIS

 * '''Installing the generator'''
   * MolgenisOnWindows -- How to setup the generator on Microsoft Windows
   * MolgenisOnUbuntu -- How to setup the generator on Ubuntu Linux
   * MolgenisOnEclipse -- How to get a useful Eclipse installed

 * '''Using the generator''' -- autogenerating your base application
   * MolgenisWorkspaceBasics -- How to open a MOLGENIS workspace
   * MolgenisGeneratorBasics -- How to use the generator
   * MolgenisAddressBookExample -- How to generate a new MOLGENIS from scratch
   * MolgenisFromExisting -- How to generate a MOLGENIS from an existing database

 * '''Using the XML language''' -- details on MOLGENIS modeling language
   * MolgenisLanguageReference -- How to use the language elements
   * MolgenisDtd -- Language definition

 * '''Using the plugin framework''' -- enhancing your MOLGENIS with handwritten components
   * MolgenisPlugin -- How to add a plugin to your MOLGENIS
   * MolgenisDatabase -- How to use the MOLGENIS database backend from your plugin
   * MolgenisEmail -- How to send emails from your MOLGENIS
   * [http://gbic.target.rug.nl:8080/hudson/job/molgenis/ws/3.3/build/javadoc/index.html MolgenisJavaDoc] -- Overview of the MOLGENIS components
   * MolgenisCustomCommand -- How to add custom buttons/dialogs to the generated forms

 * '''Using the generated application'''
   * MolgenisBatchLoading -- How to import datasets from CSV files
   * MolgenisRinterface -- How to connect to your MOLGENIS via R
   * MolgenisSoapInterface -- How connect to your MOLGENIS via web services (in Taverna)

 * '''Hacks'''
   * Generate a RDF/Sparql interface
   * Generate a RDF/Sparql interface
   * Generate a RDF/Sparql interface
   * Generate a RDF/Sparql interface