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