wiki:MolgenisIndex

Version 19 (modified by Morris Swertz, 15 years ago) (diff)

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Table of Contents

    1. Molgenis-connect
    2. How to deploy Molgenis-connect in tomcat 7
  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. MOLGENIS bookshelf
  7. Running MOLGENIS from the commandline
    1. Create
    2. Import
    3. Update
    4. Generate
    5. Run
  8. MOLGENIS suite overview: modules and products
    1. = Graphical overview of modules =
  9. MOLGENIS data model mapping overview
  10. 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
  11. Download latest version from Github
  12. Download as source code
  13. MOLGENIS language definition
  14. Emaling from within your MOLGENIS application
    1. Set your email settings in 'molgenis.properties'
    2. Add the following code to your plugin
  15. Enhancements for MOLGENIS on various levels
    1. Core
    2. Generators
    3. Plugins
  16. 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
  17. 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
  18. Layout of MOLGENIS projects
  19. Subversion
  20. Extract MOLGENIS model from existing database
    1. Generating a MOLGENIS for an existing database
    2. Example
  21. MOLGENIS generator basics
  22. Join the MOLGENIS Google group
  23. MOLGENIS development manual
  24. MOLGENIS related internships
  25. Language reference
    1. Database language (*_db.xml)
    2. User interface language (*_ui.xml)
    3. DTD
  26. MOLGENIS language reference in one page (easy for searching and printing)
  27. The MOLGENIS database language knows the following elements
  28. The MOLGENIS user interface language knows the following elements
  29. Overview of MOLGENIS modules
    1. Manually curated list
    2. Automatic generated list
  30. Movies about MOLGENIS
    1. Demos
  31. Example movie
  32. Eclipse install
    1. Frequently asked questions
  33. 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'
  34. Eclipse install
    1. Frequently asked questions
  35. Get from a clean Windows install up to the point where you can …
  36. title
    1. List of Plugins
  37. Quick Molgenis polls
  38. MolgenisProcessing
    1. Use Cases
    2. PBS best practices
  39. MOLGENIS progress update Jan - Jun 2010
    1. highlights
    2. Progress
    3. Bottlenecks
    4. Scientific output
    5. Collaborations
  40. About MOLGENIS
    1. MOLGENIS Contributors
  41. MOLGENIS partners
    1. MOLGENIS Partners
  42. Overview of Projects
  43. GCC SCRUM page
  44. Backlog
    1. Compute
    2. Apps
  45. 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
  46. Selected user stories for the LifeLines research portal demo
    1. Below complete backlog of LifeLines related stories
  47. 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
  48. 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
  49. MOLGENIS Research Platform - Sprint 11.16
    1. Team 1: Research Platform
    2. Team 2: LIMS
  50. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: LifeLines
    3. Team 3: Pheno
  51. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: …
  52. FAQ for servers and VMs
    1. General
    2. Access
    3. Operating system
    4. Storage and backups
    5. Configuration
    6. Hosting
  53. MOLGENIS source code
    1. What do I need?
  54. Rapid generation of biosoftware you want to have
  55. Using MOLGENIS
  56. Getting involved
  57. MOLGENIS Users
    1. MOLGENIS is being used in the following projects:
  58. MOLGENIS Testing Framework
    1. Unit tests for Modules
    2. Integration tests
    3. UI web tests
  59. 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?
  60. Molgenis UI components
  61. Open the MOLGENIS workspace in Eclipse