BASE 2.17.2 Documentation
Table of Contents
- I. Overview
- 1. Why use BASE
- 1.1.
- 2. BASE features
- 2.1. Supported array platforms and raw data formats
- 2.1.1. Vendor specific and custom printing array
platforms
- 2.1.2. Available raw data types
- 3. Overview of BASE
- 3.1.
- 4. Resources
- 4.1. BASE project site
- 4.1.1. Download
- 4.1.2. Ticket system
- 4.1.3. Roadmap
- 4.1.4. Documentation
- 4.2. Core plug-in configurations
- 4.3. BASE plug-ins site
- 4.4. Demo server
- 4.5. Mailing lists
- 4.6. BASE-hacks
- II. User documentation
- 5. Overview of user documentation
- 5.1. Working environment
- 5.2. Start working with BASE
- 5.2.1. Get going
- 6. Using the web client
- 6.1. Introduction
- 6.1.1. Logging in
- 6.1.2. Forgotten password
- 6.1.3. The home page
- 6.1.4. Using the menu bar
- 6.1.5. Getting help
- 6.2. Configuring your account
- 6.2.1. Contact information
- 6.2.2. Other information
- 6.2.3. Changing password
- 6.2.4. Preferences
- 6.3. Working with items
- 6.3.1. Create a new item
- 6.3.2. Edit an existing item
- 6.3.3. Delete items
- 6.3.4. Restore deleted items
- 6.3.5. Share items to other users
- 6.3.6. Change owner of items
- 6.3.7. Export items
- 6.4. Listing items
- 6.4.1. Ordering the list
- 6.4.2. Filtering the list
- 6.4.3. Configuring which columns to show
- 6.4.4. Presets
- 6.5. Trashcan
- 6.5.1. Delete items permanently
- 6.5.2. View dependencies of a trashed item
- 6.6. Item overview
- 6.6.1. Validation options
- 6.6.2. Fixing validation failures
- 7. Projects and the permission system
- 7.1. The permission system
- 7.1.1. Permission levels
- 7.1.2. Getting access to an item
- 7.1.3. Plug-in permissions
- 7.2. Projects
- 7.2.1. The active project
- 7.2.2. How to give other users access to your project
- 7.2.3. Working with the items in the project
- 7.3. Permission templates
- 8. File management
- 8.1. File system
- 8.1.1. Browse the file system
- 8.1.2. Disk space quota
- 8.2. Handling files
- 8.2.1. Upload a new file
- 8.2.2. External files
- 8.2.3. Edit a file
- 8.2.4. Move files
- 8.2.5. Viewing and downloading files
- 8.2.6. Directories
- 8.3. File types
- 9. Jobs
- 9.1. Properties
- 10. Reporters
- 10.1. Introduction
- 10.2. Reporter types
- 10.3. Reporters
- 10.3.1. Import/update reporter from files
- 10.3.2. Manual management of reporters
- 10.3.3. Deleting reporters
- 10.4. Reporter lists
- 11. Annotations
- 11.1. Annotation Types
- 11.1.1. Properties
- 11.1.2. Options
- 11.1.3. Item types
- 11.1.4. Units
- 11.1.5. Categories
- 11.2. Annotation type categories
- 11.3. Best Practices and Tab2Mage Export functionality
- 11.4. Annotating items
- 11.4.1. Inheriting annotations from other items
- 11.4.2. Mass annotation import plug-in
- 12. Experimental platforms and data file types
- 12.1. Platforms
- 12.1.1. Platform variants
- 12.2. Data file types
- 13. Protocols and protocol types
- 13.1. Protocol types
- 13.2. Protocols
- 13.2.1. Protocol properties
- 13.2.2. Protocol parameters
- 14. Hardware
- 14.1. Hardware types
- 14.2. Hardware
- 15. Software
- 15.1. Software types
- 15.2. Softwares
- 16. Array LIMS
- 16.1. Plates
- 16.2. Array designs
- 16.2.1. Properties
- 16.2.2. Importing features to an array design
- 16.3. Array batches
- 16.3.1. Creating array batches
- 16.3.2. Properties
- 16.4. Array slides
- 16.4.1. Creating array slides
- 16.4.2. Properties
- 17. Biomaterial
- 17.1. Introduction
- 17.2. Biosources
- 17.2.1. Properties
- 17.3. Samples
- 17.3.1. Create sample
- 17.3.2. Properties
- 17.4. Extracts
- 17.4.1. Create extract
- 17.4.2. Properties
- 17.5. Labels
- 17.5.1. Properties
- 17.6. Labeled extracts
- 17.6.1. Creating labeled extracts
- 17.6.2. Properties
- 17.7. Bioplate
- 17.7.1. Properties
- 17.7.2. Biowell
- 17.8. Hybridizations
- 17.8.1. Creating hybridizations
- 17.8.2. Properties
- 18. Experiments and analysis
- 18.1. Scans and images
- 18.1.1. Scan properties
- 18.1.2. Images
- 18.2. Raw bioassays
- 18.2.1. Raw bioassay properties
- 18.2.2. Import raw data
- 18.2.3. Raw data types
- 18.2.4. Spot images
- 18.3. Experiments
- 18.3.1. Experiment properties
- 18.3.2. Experimental factors
- 18.3.3. Tab2Mage export
- 18.4. Analysing data within BASE
- 18.4.1. Transformations and bioassay sets
- 18.4.2. Filtering data
- 18.4.3. Normalizing data
- 18.4.4. Other analysis plug-ins
- 18.4.5. The plot tool
- 18.4.6. Experiment explorer
- 19. Import of data
- 19.1. General import procedure
- 19.1.1. Select plug-in and file format
- 19.1.2. Specify plug-in parameters
- 19.1.3. Add the import job to the job queue
- 19.2. Batch import of data
- 19.2.1. File format
- 19.2.2. Running the item batch importer
- 19.2.3. Comments on the item batch importers
- 20. Export of data
- 20.1. Select plug-in and configuration
- 20.2. Specify plug-in parameters
- 20.3. The table exporter plug-in
- III. Admin documentation
- 21. Installation, setup, migration, and upgrade instructions
- 21.1. Upgrade instructions
- 21.2. Installing job agents
- 21.2.1. BASE application server side setup
- 21.2.2. Database server setup
- 21.2.3. Job agent client setup
- 21.2.4. Configuring the job agent
- 21.3. Installation instructions
- 21.4. Server configurations
- 21.4.1. Sending a broadcast message to logged in users
- 21.5. Migration instructions
- 22. Plug-ins
- 22.1. Installing plug-ins
- 22.1.1. Select installation method
- 22.1.2. Plug-in properties
- 22.1.3. Automatic installation of plug-ins
- 22.1.4. BASE version 1 plug-ins
- 22.2. Plug-in permissions
- 22.3. Job agents
- 22.4. Plug-in configurations
- 22.4.1. Configuring plug-in configurations
- 22.4.2. Importing and exporting plug-in configurations
- 22.4.3. The Test with file function
- 22.4.4. Configuring Base1PluginExecuter
- 23. Extensions
- 23.1. Installing extensions
- 23.2. Installing the X-JSP compiler
- 23.3. Configuring the extensions system
- 23.3.1. Settings
- 23.3.2. Disable/enable extensions
- 24. Account administration
- 24.1. Users administration
- 24.1.1. Edit user
- 24.1.2. Default group and role membership
- 24.2. Groups administration
- 24.2.1. Edit group
- 24.3. Roles administration
- 24.3.1. Pre-defined system roles
- 24.3.2. Edit role
- 24.4. Disk space/quota
- 24.4.1. Edit quota
- 24.4.2. Disk usage
- IV. Developer documentation
- 25. Developer overview of BASE
- 25.1. Fixed vs. dynamic database
- 25.2. Hibernate and the DbEngine
- 25.3. The Batch API
- 25.4. Data classes vs. item classes
- 25.5. The Query API
- 25.6. The Controller API
- 25.7. Plug-ins
- 25.8. Client applications
- 26. Plug-in developer
- 26.1. How to organize your plug-in project
- 26.1.1. Using Ant
- 26.1.2. With Eclipse
- 26.1.3. Make the plug-in compatible with the auto-installation wizard
- 26.2. The Plug-in API
- 26.2.1. The main plug-in interfaces
- 26.2.2. How the BASE core interacts with the plug-in when...
- 26.2.3. Using custom JSP pages for parameter input
- 26.3. Import plug-ins
- 26.3.1. Autodetect file formats
- 26.3.2. The AbstractFlatFileImporter superclass
- 26.4. Export plug-ins
- 26.4.1. Immediate download of exported data
- 26.4.2. The AbstractExporterPlugin class
- 26.5. Analysis plug-ins
- 26.5.1. The AbstractAnalysisPlugin class
- 26.5.2. The AnalysisFilterPlugin interface
- 26.6. Other plug-ins
- 26.6.1. Authentication plug-ins
- 26.6.2. Secondary file storage plugins
- 26.6.3. File unpacker plug-ins
- 26.6.4. File packer plug-ins
- 26.6.5. File validator and metadata reader plug-ins
- 26.6.6. Logging plug-ins
- 26.7. Enable support for aborting a running a plug-in
- 26.8. How BASE load plug-in classes
- 26.9. Example plug-ins (with download)
- 27. Extensions developer
- 27.1. Overview
- 27.1.1. Download code examples
- 27.1.2. Terminology
- 27.2. Hello world as an extension
- 27.2.1. Extending multiple extension points with a single extension
- 27.3. Custom action factories
- 27.4. Custom images, JSP files, and other resources
- 27.4.1. Javascript and stylesheets
- 27.4.2. X-JSP files
- 27.5. Custom renderers and renderer factories
- 27.6. Extension points
- 27.6.1. Error handlers
- 27.7. Custom servlets
- 28. Web services
- 28.1. Available services
- 28.1.1. Services
- 28.2. Client development
- 28.2.1. Receiving files
- 28.3. Services development
- 28.3.1. Generate WSDL-files
- 28.4. Example web service client (with download)
- 29. API overview (how to use and code examples)
- 29.1. The Public API of BASE
- 29.1.1. What is backwards compatibility?
- 29.2. The database schema and the Data Layer API
- 29.2.1. Basic classes and interfaces
- 29.2.2. User authentication and access control
- 29.2.3. Hardware and software
- 29.2.4. Reporters
- 29.2.5. Quota and disk usage
- 29.2.6. Client, session and settings
- 29.2.7. Files and directories
- 29.2.8. Experimental platforms
- 29.2.9. Parameters
- 29.2.10. Annotations
- 29.2.11. Protocols
- 29.2.12. Plug-ins, jobs and job agents
- 29.2.13. Biomaterial LIMS
- 29.2.14. Array LIMS - plates
- 29.2.15. Array LIMS - arrays
- 29.2.16. Hybridizations and raw data
- 29.2.17. Experiments and analysis
- 29.2.18. Other classes
- 29.3. The Core API
- 29.3.1. Using files to store data
- 29.3.2. Sending signals (to plug-ins)
- 29.4. The Query API
- 29.5. Analysis and the Dynamic and Batch API:s
- 29.6. Extensions API
- 29.6.1. The core part
- 29.6.2. The web client part
- 29.7. Other useful classes and methods
- 30. Write documentation
- 30.1. User, administrator and developer documentation with Docbook
- 30.1.1. Documentation layout
- 30.1.2. Getting started
- 30.1.3. Docbook tags to use
- 30.2. Create UML diagrams with MagicDraw
- 30.2.1. Organisation
- 30.2.2. Classes
- 30.2.3. Diagrams
- 30.3. Javadoc
- 30.3.1. Writing Javadoc
- 31. Core developer reference
- 31.1. Publishing a new release
- 31.2. Subversion / building BASE
- 31.3. Coding rules and guidelines
- 31.3.1. Development process and other important procedures
- 31.3.2. General coding style guidelines
- 31.3.3. API changes and backwards compatibility
- 31.3.4. Data-layer rules
- 31.3.5. Item-class rules
- 31.3.6. Batch-class rules
- 31.3.7. Test-class rules
- 31.4. Internals of the Core API
- 31.4.1. Authentication and sessions
- 31.4.2. Access permissions
- 31.4.3. Data validation
- 31.4.4. Transaction handling
- 31.4.5. Create/read/write/delete operations
- 31.4.6. Batch operations
- 31.4.7. Quota
- 31.4.8. Plugin execution / job queue
- V. FAQ
- 32. Frequently Asked Questions with answers
- 32.1. Reporter related questions with answers
- 32.2. Array design related questions with answers
- 32.3. Biomaterial, Protocol, Hardware, Software related questions with answers
- 32.4. Data Files and Raw Data related questions with answers
- 32.5. Data Deposition to Public Repositories related questions with answers
- 32.6. Analysis related questions with answers
- VI. Appendix
- A. Menu guide
- B. Core plug-ins shipped with BASE
- B.1. Core analysis plug-ins
- B.2. Core export plug-ins
- B.3. Core import plug-ins
- B.3.1. Core batch import plug-ins
- B.4. Core intensity plug-ins
- B.5. Uncategorized core plug-ins
- C. base.config reference
- D. extended-properties.xml reference
- E. Platforms and raw-data-types.xml reference
- E.1. Default platforms/variants installed with BASE
- E.2. raw-data-types.xml reference
- F. web.xml reference
- G. jobagent.properties reference
- H. jobagent.sh reference
- I. migrate.properties reference
- I.1. mysql-migration-queries.sql
- J. Other configuration files
- J.1. mysql-queries.xml and postgres-queries.xml
- J.2. log4.properties
- J.2.1. Migration logger
- J.3. hibernate.cfg.xml
- J.4. ehcache.xml
- K. API changes that may affect backwards compatibility
- K.1. BASE 2.17 release
- K.2. BASE 2.16 release
- K.3. BASE 2.15 release
- K.4. BASE 2.13 release
- K.5. BASE 2.12 release
- K.6. BASE 2.11 release
- K.7. BASE 2.10 release
- K.8. BASE 2.9 release
- K.9. BASE 2.7.1 release
- K.10. BASE 2.7 release
- K.11. BASE 2.6 release
- K.12. BASE 2.5 release
- K.13. BASE 2.4 release
- K.14. BASE 2.3 release
- K.15. BASE 2.2 release
- L. Things to consider when updating an existing BASE installation
- L.1. BASE 2.9 release
- L.2. BASE 2.7.2 release
- L.3. BASE 2.7 release
- L.4. BASE 2.4.4 release
- M. File formats
- M.1. The BFS (BASE File Set) format
- M.1.1. The basics of BFS
- M.1.2. Using BFS for spotdata to and from external plug-ins
- M.2. The BASEfile format
- M.2.1. To be done