Part II. User documentation

Table of Contents

5. Overview of user documentation
5.1. Working environment
5.2. Start working with BASE
5.2.1. Get going
Administrative tasks
User tasks
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
The Appearance tab
The Plugins tab
The Recent items tab
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
Units
6.4.3. Configuring which columns to show
6.4.4. Presets
Save a preset
Manage presets
6.5. Trashcan
6.5.1. Delete items permanently
Empty trashcan
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
Selecting an active project
Default permissions for 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
Navigation tree
8.1.2. Disk space quota
8.2. Handling files
8.2.1. Upload a new file
Replace an existing file
8.2.2. External files
File servers
8.2.3. Edit a file
8.2.4. Move files
To another directory
Offline
To the secondary storage
8.2.5. Viewing and downloading files
Download a file
View the contents of file
Download/compress multiple files
8.2.6. Directories
Edit a directory
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
Reporter properties
Extended properties
10.3.3. Deleting reporters
Batch deletion
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
Array design
Annotations and inherited annotations
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
Multiple slides wizard
17. Biomaterial
17.1. Introduction
17.2. Biosources
17.2.1. Properties
Biosource
Annotations
17.3. Samples
17.3.1. Create sample
17.3.2. Properties
Sample
Parents
Annotations & parameters
Inherited annotations
17.4. Extracts
17.4.1. Create extract
17.4.2. Properties
Extract
Parents
Annotations & parameters
Inherited Annotations
17.5. Labels
17.5.1. Properties
17.6. Labeled extracts
17.6.1. Creating labeled extracts
17.6.2. Properties
Labeled extract
Parents
Annotations & parameters
Inherited annotations
17.7. Bioplate
17.7.1. Properties
Annotations
17.7.2. Biowell
Properties
17.8. Hybridizations
17.8.1. Creating hybridizations
17.8.2. Properties
Hybridization
Labeled extracts
Annotations & parameters
Inherited annotations
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
File-only platforms
18.2.4. Spot images
18.3. Experiments
18.3.1. Experiment properties
The publication tab
18.3.2. Experimental factors
18.3.3. Tab2Mage export
Biomaterial annotations
Annotation units
Protocol parameters
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