wiki:MolgenisIndex
Last modified 2 years ago

Table of Contents

  1. Generating MOLGENIS from scratch, the Address Book Example
    1. 1. Create the data model in addressbook_db.xml
      1. Create a “Contact” data type
      2. Add properties to “Contact”
      3. Create a “Address” data type
      4. Link Addresses to Contact.
    2. 2. Model the user interface in addressbook_ui.xml
    3. Generate the application
      1. Configure the molgenis.properties file.
      2. Create an addressbook mysql instance
      3. Generate and compile your database
    4. 3. Expected result
  2. Stories for the research portal release of 31 dec 2011
  3. MOLGENIS Apps
    1. For researchers
    2. For developers
    3. Getting started
    4. Description of all project elements
      1. build scripts
      2. /apps
      3. /modules
      4. /generated (svn:ignore)
      5. /WebContent
      6. /dist (svn:ignore)
    5. Creating a new app
  4. Architecture overview
  5. Using Molgenis as a datasource for Galaxy
  6. Batch loading of data
    1. Loading csv data using the UI
      1. Load data for Contact.
      2. Load data for Address, including 'xref by name'
  7. MOLGENIS bookshelf
  8. Running MOLGENIS from the commandline
    1. Create
    2. Import
    3. Update
    4. Generate
    5. Run
  9. MOLGENIS suite overview: modules and products
    1. = Graphical overview of modules =
  10. Adding Custom buttons to the generated code
    1. 1. Define the custom commands in your *ui.xml
    2. 2. Implement the button
  11. MOLGENIS data model mapping overview
  12. Accessing the database via Molgenis Database
    1. In a standalone program
  13. Database API
    1. Get a database
    2. Add objects in batch
    3. Queries made simple
    4. Shorthand for query by primary key (id)
  14. How to deploy a MOLGENIS project under a different name
    1. Project name
    2. Database name
    3. Deploy name
    4. Optional: add or remove security
    5. Final note
  15. Documentation
    1. MOLGENIS Apps
    2. MOLGENIS framework
    3. Standard operation procedures (private)
  16. Download latest version from Subversion
  17. Download Eclipse workspace from sourceforge
  18. Download as source code
  19. MOLGENIS language definition
  20. <molgenis>
    1. Required attributes
    2. Optional attributes
    3. Child elements
  21. Emaling from within your MOLGENIS application
    1. Set your email settings in 'molgenis.properties'
    2. Add the following code to your plugin
  22. Enhancements for MOLGENIS on various levels
    1. Core
    2. Generators
    3. Plugins
  23. MOLGENIS FAQ
    1. Customizing look & layout
    2. Statement.GeneratedKeysNotRequested?
    3. It doesn't work after checkout!
    4. I want to automatically select my plugin
    5. Create new MOLGENIS project
    6. Can/should I use Infobright / Brigthouse for big data
    7. How to remove *.svn directories
  24. MolgenisFile
    1. Overview
      1. Field is file
      2. Entity is file
    2. Merging
    3. Technical
      1. Decorating
      2. Setting storage location
      3. Java API
      4. Services: uploading and downloading
      5. Practical example
      6. Java API extension example
    4. Notes
  25. Layout of MOLGENIS projects
  26. Subversion
  27. Extract MOLGENIS model from existing database
    1. Generating a MOLGENIS for an existing database
    2. Example
  28. MOLGENIS generator basics
  29. Join the MOLGENIS Google group
  30. MOLGENIS development manual
  31. MOLGENIS related internships
  32. Introduction
    1. Why MOLGENIS?
    2. What will you achieve with this guide?
  33. MOLGENIS Java Doc
  34. Language reference
    1. Database language (*_db.xml)
    2. User interface language (*_ui.xml)
    3. DTD
  35. MOLGENIS language reference in one page (easy for searching and printing)
  36. The MOLGENIS database language knows the following elements
  37. The MOLGENIS user interface language knows the following elements
  38. Overview of MOLGENIS modules
    1. Manually curated list
    2. Automatic generated list
  39. Movies about MOLGENIS
    1. Demos
  40. Example movie
  41. Eclipse install
    1. Frequently asked questions
  42. How to develop MOLGENIS on Eclipse/Helios?
    1. 1. Install eclipse helios
    2. 2. install SVN plugin 'subclipse'
    3. 3. install freemarker plugin 'Freemarker IDE'
    4. 4. checkout molgenis projects
    5. 5. Develop
    6. FAQ
      1. Q1: how to add/manage J2EE dependencies
      2. Q2: I get 404 errors when starting the server
      3. Q3: I get a very long 'loading web service DOM'
  43. Getting MOLGENIS running on Ubuntu
    1. Installing Ubuntu inside Windows using VirtualBox
    2. Install MySQL, Tomcat, Java, Eclipse on Ubuntu
  44. 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
  45. 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'
      1. Edit the reload function to produce a pubmed query URL
    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
  46. title
    1. List of Plugins
  48. Quick Molgenis polls
  49. MolgenisProcessing
    1. Use Cases
    2. PBS best practices
  50. MOLGENIS progress update Jan - Jun 2010
    1. highlights
    2. Progress
    3. Bottlenecks
    4. Scientific output
    5. Collaborations
  51. About MOLGENIS
    1. MOLGENIS Contributors
  52. MOLGENIS partners
    1. MOLGENIS Partners
  53. Overview of Projects
  54. molgenis.properties file
    1. molgenis.passwd file
  55. How to rename a MOLGENIS project in Eclipse
    1. Step 1: Checkout MOLGENIS distro
    2. Step 2: Disconnect from SVN
    3. Step 3: Rename the web address
    4. Step 4: Regenerate your MOLGENIS as usual
  56. Posting data to MOLGENIS using REST API
    1. Using simple GET commands
    2. Using CURL
  57. Using the R interface
  58. GCC SCRUM page
    1. Sprints
    2. Demos
  59. Backlog
  60. Notes from End-of-sprint demo 11.27, July 4 2011
    1. Report of Team 2, Sprint 7, 11.27
      1. Story: directory structure.
      2. Story: LifeLines import into Oracle
      3. Story: OSGi pilot …
      4. Story: BBMRI catalogue user want simpler search and download
    2. Report of team 1
  61. Selected user stories for the LifeLines research portal demo
    1. Below complete backlog of LifeLines related stories
  62. MOLGENIS Research Platform - Sprint 1
    1. Lessons learned
    1. MOLGENIS Research Platform - Sprint 2
    2. User stories selected by Matrix team
    3. User stories selected by Protocol team
    4. User stories moved to the Sprint Backlog
    5. Lessons Learnt from evaluation session of Sprint 2 on Mar. 3rd
  64. MOLGENIS Research Platform - Sprint 11.12
    1. Lessons Learnt from evaluation session of Sprint 3 (11.12) on Mar. 25th
    2. User story suggestions from end-of-sprint demo's
  65. MOLGENIS Research Platform - Sprint 11.16
    1. Team 1: Research Platform
    2. Team 2: LIMS
  66. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: LifeLines
    3. Team 3: Pheno
  67. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: …
  68. List of MOLGENIS servers
  69. List of MOLGENIS test servers
  70. FAQ for servers and VMs
    1. General
    2. Access
    3. Operating system
    4. Storage and backups
    5. Configuration
    6. Hosting
  71. SOPs
  72. Discussion
  73. Using the SOAP interface in Taverna
  74. MOLGENIS source code
    1. What do I need?
    2. What is in the other packages?
  75. Rapid generation of biosoftware you want to have
  76. Using MOLGENIS
  77. Getting involved
  78. MOLGENIS Users
    1. MOLGENIS is being used in the following projects:
  80. MOLGENIS Testing Framework
    1. Unit tests for Modules
    2. Integration tests
    3. UI web tests
  81. How to make good tickets?
    1. What is a ticket?
    2. What makes a good ticket?
    3. Size of tickets?
    4. How to use Milestones?
    5. What ticket type to use?
  82. Molgenis UI components
  83. Manual for Molgenis UI components
    1. How to make your plugin Freemarker-less
    2. What components to choose from
      1. The most important components
      2. Components that seem to offer no added value at this moment
      3. Components that should not be used at the moment
      4. Desired components
    3. How to integrate the components into your plugin
    4. Fancy JavaScript actions
    5. Code example
  84. Using the user interface
  85. Open the MOLGENIS workspace in Eclipse