1. Introduction
   1. Introduction
      1. Why MOLGENIS?
      2. What will you achieve with this guide?

2. Installation
   1. Get from a clean Windows install up to the point where you can generate, …
      1. Install Java,Tomcat,MySQL and Eclipse
      2. Create a database in MySQL
      3. Open the MOLGENIS workspace using Eclipse
   2. Getting MOLGENIS running on Ubuntu
      1. Installing Ubuntu inside Windows using VirtualBox
      2. Install MySQL, Tomcat, Java, Eclipse on Ubuntu
   3. Eclipse install
      1. Frequently asked questions

3. Generation
   1. Open the MOLGENIS workspace in Eclipse
   2. MOLGENIS generator basics
   3. Generating MOLGENIS from scratch, the Address Book Example
      1. 1. Create the data model in addressbook_db.xml
      2. 2. Model the user interface in addressbook_ui.xml
      3. Generate the application
      4. 3. Expected result
   4. Extract MOLGENIS model from existing database
      1. Generating a MOLGENIS for an existing database
      2. Example
   5. Language reference
      1. Database language (*_db.xml)
      2. User interface language (*_ui.xml)
      3. DTD
   6. MOLGENIS language definition

4. Application
   1. Using the user interface
   2. Batch loading of data
      1. Loading csv data using the UI
   3. Using the R interface
   4. Using the SOAP interface in Taverna

5. Plugins
   1. Creating a user interface plug-in
      1. 1. Define the plugin in the 'addressbook_ui.xml'
      2. 2. Add reload logic to 'plugin.pubmed.PubmedPlugin.java'
      3. 3. Create a html layout in plugin.pubmed.PubmedPlugin.ftl to show Pubmed …
      4. 4. Add user input handling to enable users to choose year
   2. Accessing the database via Molgenis Database
      1. In a standalone program
   3. Emaling from within your MOLGENIS application
      1. Set your email settings in 'molgenis.properties'
      2. Add the following code to your plugin