wiki:MolgenisIndex

Version 20 (modified by Morris Swertz, 15 years ago) (diff)

Name changed from DocIndex? to MolgenisIndex

Table of Contents

    1. Molgenis-connect
    2. How to deploy Molgenis-connect in tomcat 7
  2. 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
  3. Stories for the research portal release of 31 dec 2011
  4. 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
  5. Architecture overview
  6. Using Molgenis as a datasource for Galaxy
  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. MOLGENIS data model mapping overview
  11. 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
  12. Download latest version from Github
  13. Download as source code
  14. MOLGENIS language definition
  15. Emaling from within your MOLGENIS application
    1. Set your email settings in 'molgenis.properties'
    2. Add the following code to your plugin
  16. Enhancements for MOLGENIS on various levels
    1. Core
    2. Generators
    3. Plugins
  17. 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
  18. 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
  19. Layout of MOLGENIS projects
  20. Subversion
  21. Extract MOLGENIS model from existing database
    1. Generating a MOLGENIS for an existing database
    2. Example
  22. MOLGENIS generator basics
  23. Join the MOLGENIS Google group
  24. MOLGENIS development manual
  25. MOLGENIS related internships
  26. Language reference
    1. Database language (*_db.xml)
    2. User interface language (*_ui.xml)
    3. DTD
  27. MOLGENIS language reference in one page (easy for searching and printing)
  28. The MOLGENIS database language knows the following elements
  29. The MOLGENIS user interface language knows the following elements
  30. Overview of MOLGENIS modules
    1. Manually curated list
    2. Automatic generated list
  31. Movies about MOLGENIS
    1. Demos
  32. Example movie
  33. Eclipse install
    1. Frequently asked questions
  34. 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'
  35. Eclipse install
    1. Frequently asked questions
  36. Get from a clean Windows install up to the point where you can …
  37. title
    1. List of Plugins
  39. Quick Molgenis polls
  40. MolgenisProcessing
    1. Use Cases
    2. PBS best practices
  41. MOLGENIS progress update Jan - Jun 2010
    1. highlights
    2. Progress
    3. Bottlenecks
    4. Scientific output
    5. Collaborations
  42. About MOLGENIS
    1. MOLGENIS Contributors
  43. MOLGENIS partners
    1. MOLGENIS Partners
  44. Overview of Projects
  45. GCC SCRUM page
  46. Backlog
    1. Compute
    2. Apps
  47. 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
  48. Selected user stories for the LifeLines research portal demo
    1. Below complete backlog of LifeLines related stories
  49. 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
  51. 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
  52. MOLGENIS Research Platform - Sprint 11.16
    1. Team 1: Research Platform
    2. Team 2: LIMS
  53. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: LifeLines
    3. Team 3: Pheno
  54. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: …
  55. FAQ for servers and VMs
    1. General
    2. Access
    3. Operating system
    4. Storage and backups
    5. Configuration
    6. Hosting
  56. MOLGENIS source code
    1. What do I need?
  57. Rapid generation of biosoftware you want to have
  58. Using MOLGENIS
  59. Getting involved
  60. MOLGENIS Users
    1. MOLGENIS is being used in the following projects:
  62. MOLGENIS Testing Framework
    1. Unit tests for Modules
    2. Integration tests
    3. UI web tests
  63. 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?
  64. Molgenis UI components
  65. Open the MOLGENIS workspace in Eclipse