BASE 3.1.2 Documentation

Last modified: 2012-02-23


Table of Contents

I. Overview
1. Why use BASE
1.1. Case I: The SCAN-B BASE installation at Department of Oncology, Lund University
1.2. Case II: The BASE installation at SCIBLU, Department of Oncology, Lund University
2. BASE features
2.1. Web interface
2.2. Information and annotation management
2.3. Data sharing and privacy
2.4. File and directory structure
2.5. Plugin and extension infrastructure
2.6. Batch upload and download of data
2.7. Supported array platforms and raw data formats
2.7.1. Vendor specific and custom printing array platforms
2.7.2. Available raw data types
2.8. Supported sequencing applications
2.9. Repository and standards
3. Resources
3.1. BASE project site
3.1.1. Download
3.1.2. Ticket system
3.1.3. Roadmap
3.1.4. Documentation
3.2. BASE plug-ins site
3.3. Demo server
3.4. Mailing lists
3.5. BASE-hacks
II. User documentation
4. Overview of user documentation
4.1. Working environment
4.2. Start working with BASE
4.2.1. Administrative tasks
4.2.2. User tasks
5. Using the web client
5.1. Introduction
5.1.1. Logging in
5.1.2. Forgotten password
5.1.3. The home page
5.1.4. Using the menu bar
5.1.5. Getting help
5.2. Configuring your account
5.2.1. Contact information
5.2.2. Other information
5.2.3. Changing password
5.2.4. Preferences
5.3. Working with items
5.3.1. Create a new item
5.3.2. Edit an existing item
5.3.3. Delete items
5.3.4. Restore deleted items
5.3.5. Share items to other users
5.3.6. Change owner of items
5.4. Listing items
5.4.1. Ordering the list
5.4.2. Filtering the list
5.4.3. Configuring which columns to show
5.4.4. Presets
5.5. Trashcan
5.5.1. Delete items permanently
5.5.2. View dependencies of a trashed item
5.6. Item overview
5.6.1. Validation options
5.6.2. Fixing validation failures
6. Projects and the permission system
6.1. The permission system
6.1.1. Permission levels
6.1.2. Getting access to an item
6.1.3. Plug-in permissions
6.2. Projects
6.2.1. Creating a project
6.2.2. The active project
6.2.3. How to give other users access to your project
6.2.4. Default items
6.2.5. Working with the items in the project
6.3. Permission templates
7. File management
7.1. File system
7.1.1. Disk space quota
7.2. Handling files
7.2.1. Upload a new file
7.2.2. External files
7.2.3. File servers
7.2.4. Edit a file
7.2.5. Move files
7.2.6. Viewing and downloading files
7.2.7. Directories
8. Jobs
9. Reporters
9.1. Reporter types
9.2. Reporters
9.2.1. Import/update reporter from files
9.2.2. Manual management of reporters
9.2.3. Deleting reporters
9.3. Reporter lists
9.3.1. Merging reporter lists
10. Annotations
10.1. Annotation Types
10.1.1. Properties
10.1.2. Options
10.1.3. Item types
10.1.4. Units
10.1.5. Categories
10.2. Annotating items
10.2.1. Inheriting annotations from other items
10.2.2. Mass annotation import plug-in
11. Experimental platforms and data file types
11.1. Platforms
11.2. Platform variants
11.3. Data file types
11.4. Selecting files for an item
12. Item subtypes
12.1. Item subtype properties
12.2. File types
13. Protocols
13.1. Protocol parameters
14. Hardware and software
14.1. Hardware
14.2. Software
15. Array LIMS
15.1. Array designs
15.1.1. Properties
15.1.2. Importing features to an array design
15.2. Array batches
15.3. Array slides
15.3.1. Creating array slides
15.3.2. Multiple slides wizard
16. Biomaterial LIMS
16.1. Biosources
16.2. Samples
16.2.1. Create sample
16.2.2. Sample properties
16.2.3. Sample parents
16.3. Extracts
16.3.1. Create extract
16.3.2. Extract properties
16.3.3. Extract parents
16.4. Tags
16.5. Bioplates
16.5.1. Bioplate properties
16.5.2. Biowells
16.5.3. Bioplate types
16.5.4. Bioplate events
16.6. Biomaterial lists
16.7. Physical bioassays
16.7.1. Create physical bioassays
16.7.2. Bioassay properties
16.7.3. Parent extracts
17. Experiments and analysis
17.1. Derived bioassays
17.1.1. Create derived bioassays
17.1.2. Derived bioassay properties
17.2. Raw bioassays
17.2.1. Create raw bioassays
17.2.2. Raw bioassay properties
17.2.3. Import raw data
17.2.4. Raw data types
17.2.5. Spot images
17.3. Experiments
17.3.1. Experiment properties
17.3.2. Experimental factors
17.4. Analysing data within BASE
17.4.1. Transformations and bioassay sets
17.4.2. Filtering data
17.4.3. Normalizing data
17.4.4. Other analysis plug-ins
17.4.5. The plot tool
17.4.6. Experiment explorer
18. Import of data
18.1. General import procedure
18.1.1. Select plug-in and file format
18.1.2. Specify plug-in parameters
18.1.3. Add the import job to the job queue
18.2. Batch import of data
18.2.1. File format
18.2.2. Running the item batch importer
18.2.3. Comments on the item batch importers
19. Export of data
19.1. Select plug-in and configuration
19.2. Specify plug-in parameters
19.3. The table exporter plug-in
III. Admin documentation
20. Installation and upgrade instructions
20.1. Upgrade instructions
20.2. Installation instructions
20.3. Installing job agents
20.3.1. BASE application server side setup
20.3.2. Database server setup
20.3.3. Job agent client setup
20.3.4. Configuring the job agent
20.4. Server configurations
20.4.1. Sending a broadcast message to logged in users
20.5. Migrating from MySQL to PostgreSQL
21. Plug-ins and extensions
21.1. Managing plug-ins and extensions
21.1.1. Automatic installation wizard
21.1.2. Manual plug-in registration
21.1.3. BASE version 1 plug-ins
21.1.4. Installing the X-JSP compiler
21.1.5. Disable/enable plug-ins and extensions
21.1.6. Plug-in permissions
21.2. Plug-in configurations
21.2.1. Configuring plug-in configurations
21.2.2. Importing and exporting plug-in configurations
21.2.3. The Test with file function
22. Account administration
22.1. Users administration
22.1.1. Edit user
22.1.2. Default group and role membership
22.2. Groups administration
22.2.1. Edit group
22.3. Roles administration
22.3.1. Pre-defined system roles
22.3.2. Edit role
22.4. Disk space/quota
22.4.1. Edit quota
22.4.2. Disk usage
IV. Developer documentation
23. Migrating code from BASE 2 to BASE 3
23.1. Compiling the code against BASE 3
23.2. Core API changes
23.3. Packaging your plug-in so that it installs in BASE 3
24. Developer overview of BASE
24.1. Fixed vs. dynamic database
24.2. Hibernate and the DbEngine
24.3. The Batch API
24.4. Data classes vs. item classes
24.5. The Query API
24.6. The Controller API
24.7. The Extensions API
24.8. Plug-ins
24.9. Client applications
25. Plug-in developer
25.1. How to organize your plug-in project
25.1.1. Using Ant
25.1.2. Make the plug-in compatible with the auto-installation wizard
25.2. The Plug-in API
25.2.1. The main plug-in interfaces
25.2.2. How the BASE core interacts with the plug-in when...
25.2.3. Abort a running a plug-in
25.2.4. Using custom JSP pages for parameter input
25.3. Import plug-ins
25.3.1. Autodetect file formats
25.3.2. The AbstractFlatFileImporter superclass
25.4. Export plug-ins
25.4.1. Immediate download of exported data
25.4.2. The AbstractExporterPlugin class
25.5. Analysis plug-ins
25.5.1. The AbstractAnalysisPlugin class
25.5.2. The AnalysisFilterPlugin interface
25.6. Other plug-ins
25.6.1. Authentication plug-ins
25.6.2. Secondary file storage plugins
25.6.3. File unpacker plug-ins
25.6.4. File packer plug-ins
25.6.5. Logging plug-ins
25.7. How BASE load plug-in classes
25.8. Example plug-ins (with download)
26. Extensions developer
26.1. Overview
26.1.1. Download code examples
26.1.2. Terminology
26.2. Hello world as an extension
26.2.1. Extending multiple extension points with a single extension
26.3. Custom action factories
26.4. Custom images, JSP files, and other resources
26.4.1. Javascript and stylesheets
26.4.2. X-JSP files
26.5. Custom renderers and renderer factories
26.6. Extension points
26.6.1. Error handlers
26.7. Custom servlets
26.8. Extension points defined by BASE
26.8.1. Menu: extensions
26.8.2. Toolbars
26.8.3. Edit dialogs
26.8.4. Bioassay set: Tools
26.8.5. Bioassay set: Overview plots
26.8.6. Services
26.8.7. Connection managers
26.8.8. Fileset validators
27. Web services
27.1. Available services
27.1.1. Services
27.2. Client development
27.2.1. Receiving files
27.3. Services development
27.3.1. Generate WSDL-files
27.4. Example web service client (with download)
28. The BASE API
28.1. The Public API of BASE
28.1.1. What is backwards compatibility?
28.2. The Data Layer API
28.2.1. Basic classes and interfaces
28.2.2. User authentication and access control
28.2.3. Reporters
28.2.4. Quota and disk usage
28.2.5. Client, session and settings
28.2.6. Files and directories
28.2.7. Experimental platforms and item subtypes
28.2.8. Parameters
28.2.9. Annotations
28.2.10. Protocols, hardware and software
28.2.11. Plug-ins, jobs and job agents
28.2.12. Biomaterial LIMS
28.2.13. Array LIMS - plates
28.2.14. Array LIMS - arrays
28.2.15. Bioassays and raw data
28.2.16. Experiments and analysis
28.2.17. Other classes
28.3. The Core API
28.3.1. Authentication and sessions
28.3.2. Access permissions
28.3.3. Data validation
28.3.4. Transaction handling
28.3.5. Create/read/write/delete operations
28.3.6. Batch operations
28.3.7. Quota
28.3.8. Plugin execution / job queue
28.3.9. Using files to store data
28.3.10. Sending signals (to plug-ins)
28.4. The Query API
28.5. The Dynamic API
28.6. The Extensions API
28.6.1. The core part
28.6.2. The web client part
28.7. Other useful classes and methods
29. Write documentation
29.1. User, administrator and developer documentation with Docbook
29.1.1. Documentation layout
29.1.2. Getting started
29.1.3. Docbook tags to use
29.2. Create UML diagrams with MagicDraw
29.2.1. Organisation
29.2.2. Classes
29.2.3. Diagrams
29.3. Javadoc
29.3.1. Writing Javadoc
30. Core developer reference
30.1. Publishing a new release
30.2. Subversion / building BASE
30.3. Coding rules and guidelines
30.3.1. Development process and other important procedures
30.3.2. General coding style guidelines
30.3.3. API changes and backwards compatibility
30.3.4. Data-layer rules
30.3.5. Item-class rules
30.3.6. Batch-class rules
30.3.7. Test-class rules
V. FAQ
31. Frequently Asked Questions with answers
31.1. Reporter related questions with answers
31.2. Array design related questions with answers
31.3. Biomaterial, Protocol, Hardware, Software related questions with answers
31.4. Data Files and Raw Data related questions with answers
31.5. Analysis related questions with answers
VI. Appendix
A. Core plug-ins shipped with BASE
A.1. Core analysis plug-ins
A.2. Core export plug-ins
A.3. Core import plug-ins
A.3.1. Core batch import plug-ins
A.4. Core intensity plug-ins
A.5. Uncategorized core plug-ins
B. base.config reference
C. extended-properties.xml reference
D. Platforms and raw-data-types.xml reference
D.1. Default platforms and variants installed with BASE
D.2. raw-data-types.xml reference
E. web.xml reference
F. jobagent.properties reference
G. jobagent.sh reference
H. Other configuration files
H.1. mysql-queries.xml and postgres-queries.xml
H.2. log4j.properties
H.3. hibernate.cfg.xml
H.4. ehcache.xml
I. API changes that may affect backwards compatibility
I.1. BASE 3.1 release
I.2. BASE 3.0 release
I.3. All BASE 2.x releases
J. Things to consider when updating an existing BASE installation
J.1. All BASE 2.x releases
K. File formats
K.1. The BFS (BASE File Set) format
K.1.1. The basics of BFS
K.1.2. Using BFS for spotdata to and from external plug-ins
K.2. The BASEfile format
K.2.1. To be done