Part II. User documentation

Table of Contents

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
The Appearance tab
The Plugins tab
The Recent items tab
The Inactive roles tab
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
Extending the search with multiple filter rows
Units
5.4.3. Configuring which columns to show
5.4.4. Presets
Save a preset
Manage presets
5.5. Trashcan
5.5.1. Delete items permanently
Empty trashcan
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
Selecting an active project
Default permissions for 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
Replace an existing file
7.2.2. External files
7.2.3. File servers
7.2.4. Edit a file
7.2.5. Move files
To another directory
Offline
To the secondary storage
7.2.6. Viewing and downloading files
Download a file
View the contents of file
Download/compress multiple 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
Batch deletion
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. Project-specific annotations
10.2.2. Inheriting annotations from other items
10.2.3. Batch inherit annotations
10.2.4. 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
The place-on-plate event
The move biomaterials event
The create child plate event
16.6. Physical bioassays
16.6.1. Create physical bioassays
16.6.2. Bioassay properties
16.6.3. Parent extracts
17. Item lists
17.1. Manage list members manually
17.2. Merging lists
17.3. Synchronization filters
18. Experiments and analysis
18.1. Derived bioassays
18.1.1. Create derived bioassays
18.1.2. Derived bioassay properties
18.2. Raw bioassays
18.2.1. Create raw bioassays
18.2.2. Raw bioassay properties
18.2.3. Import raw data
18.2.4. Raw data types
File-only platforms
18.2.5. Spot images
18.3. Experiments
18.3.1. Experiment properties
The publication tab
18.3.2. Experimental factors
18.4. Analysing data within BASE
18.4.1. Transformations and bioassay sets
The root bioassay set
Overview plots
18.4.2. Filtering data
Formulas
18.4.3. Normalizing data
18.4.4. Other analysis plug-ins
18.4.5. The plot tool
Scatter plots
Histogram plots
Filtering plots
Save plots
18.4.6. Experiment explorer
Reporter view
Reporter search
19. Import of data
19.1. General import procedure
19.1.1. Select plug-in and file format
The auto detect function
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