Table of Contents

  1. Introduction
    1. Why MOLGENIS?
    2. What will you achieve with this guide?
  2. 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
  3. Getting MOLGENIS running on Ubuntu
    1. Installing Ubuntu inside Windows using VirtualBox
    2. Install MySQL, Tomcat, Java, Eclipse on Ubuntu
  4. Eclipse install
  5. Open the MOLGENIS workspace in Eclipse
  6. MOLGENIS generator basics
  7. 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
  8. Extract MOLGENIS model from existing database
    1. Generating a MOLGENIS for an existing database
    2. Example
  9. Language reference
  10. MOLGENIS language definition
  11. 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
  12. Accessing the database via Molgenis Database
    1. In a standalone program
  13. Emaling from within your MOLGENIS application
    1. Set your email settings in 'molgenis.properties'
    2. Add the following code to your plugin
  14. Batch loading of data
    1. Loading csv data using the UI
  15. Using the R interface
  16. Using the SOAP interface in Taverna

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:

  • Using the plugin framework — enhancing your MOLGENIS with handwritten components
  • Hacks
    • Generate a RDF/Sparql interface
    • Generate a RDF/Sparql interface
    • Generate a RDF/Sparql interface
    • Generate a RDF/Sparql interface
Last modified by mswertz, 03/08/10 14:36:00 (3 days ago)