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Documentation: Version 15.2
Introduction
Print
Print Branch
Getting Started
Tutorials
- Tutorials for new users.
10 Minute Tour
- See some LabKey Server tools in action right now.
Videos
- Video resources for beginners and experts.
Install LabKey Server (Quick Install)
- Install LabKey Server with a graphical installer.
Documentation Contents
Administration
- Create new projects, configure security, advanced installation.
Collaboration
- Set up file repositories, message boards, and issue trackers.
Data and Views
- Build applications from user interface panels and views on underlying data.
Instrument Data
- Work with instrument-derived data.
Studies
- Integrate heterogeneous data in longitudinal/cohort studies.
Specimens
- Track specimens with a specimen repository.
Development
- Developer resources.
Documentation Highlights
What's New in 15.2?
- Highlighted features in the 15.2 release.
Release Notes 15.2
- Detailed feature list.
What's Next?
- Features in development for the 15.3 release.
Pages
Introduction
Install LabKey Server (Quick Install)
What's New in 15.2?
Release Notes 15.2
What's Next?
Tutorials
Videos
Presentations
Platform Overview
FAQ - Frequently Asked Questions
Platform Users
Showcase of Installations
How to Cite LabKey Server
LabKey Terminology/Glossary
Archive: Docs and Release Notes
What's New in 15.1?
Release Notes 15.1
Argos Tour
What's New in 14.3?
Release Notes 14.3
What's New in 14.2?
Release Notes 14.2
What's New in 14.1?
Release Notes 14.1
What's New in 13.3?
Release Notes 13.3
What's New in 13.2?
Release Notes 13.2
Learn What's New in 13.1
Release Notes 13.1
Video Demonstrations 13.1
New Feature "Sprint" Demos
Learn What's New in 12.3
Release Notes 12.3
12.3 Video Demonstrations
Learn What's New in 12.2
Release Notes 12.2
12.2 Video Demonstrations
Learn What's New in 12.1
12.1 Release Notes
12.1 Video Demonstrations
Learn What's New in 11.3
11.3 Release Notes
11.3 Video Demonstrations
Learn What's New in 11.2
11.2 Release Notes
11.2 Video Demonstrations
Learn What's New in 11.1
11.1 Release Notes
11.1 Release Webinar
Learn What's New in 10.3
10.3 Release Notes
Learn What's New in 10.2
10.2 Release Notes
Learn What's New in 10.1
10.1 Release Notes
Learn What's New in 9.3
9.3 Upgrade Tips
Learn What's New in 9.2
9.2 Upgrade Tips
Learn What's New in 9.1
9.1 Upgrade Tips
Learn What's New in 8.3
Learn What's New in 8.2
8.2 Upgrade Tips
Learn What's New in 8.1
8.1 Upgrade Tips
Learn What's New in 2.3
Learn What's New in 2.2
Learn What's New in 2.1
Learn What's New in 2.0
Start Here
Administration
Tutorial: Security
Step 1: Configure Permissions
Step 2: Test Security with Impersonation
Step 3: Audit User Activity
Step 4: Handle Protected Health Information (PHI)
Projects and Folders
Navigate Site
Project and Folder Basics
Site Structure: Best Practices
Manage Projects and Folders
Create a Project or Folder
Move, Delete, Rename Projects and Folders
Enable a Module in a Folder
Export / Import a Folder
Export and Import Permission Settings
Manage Email Notifications
Define Hidden Folders
Folder Types
Default Modules
Workbooks
Establish Terms of Use
Security
Configure Permissions
Security Groups
Global Groups
Project Groups
Site Groups
Guests / Anonymous Users
Security Roles Reference
Site Administrator
Matrix of Report and View Permissions
Role / Permissions Matrix
User Accounts
Add Users
Manage Users
My Account
Manage Project Users
Authentication
Configure Database Authentication
Passwords
Password Reset & Security
Configure LDAP
Configure CAS Single Sign On Authentication
Configure Duo Two Factor Authentication
Create a .netrc or _netrc file
HTTP Basic Authentication
Test Security Settings by Impersonation
Admin Console
Site Settings
Look and Feel Settings
Web Site Theme
Email Customization
Experimental Features
Manage Missing Value Indicators / Out of Range Values
Short URLs
Configure System Maintenance
Configure Scripting Engines
Audit Site Activity
Actions Diagnostics
Cache Statistics
Dump Heap
Memory Usage
Running Threads
Query Logger
Install LabKey
Installation Basics
Install LabKey Server (Windows Graphical Installer)
Install LabKey Manually
Install Required Components
Configure the LabKey Web Application
labkey.xml Configuration File Reference
Third-Party Components and Licenses
Install a Remote Pipeline Server via the Windows Installer
Supported Technologies
Troubleshoot Installation
Installation Error Messages
Dump Memory Usage Debugging Information
Common Install Tasks
Install Microsoft SQL Server
Install PostgreSQL (Windows)
Install PostgreSQL (Linux, Unix or Macintosh)
Install LabKey Server on Solaris
Notes on Installing PostgreSQL on All Platforms
Install and Set Up R
Determine Available Graphing Functions
Install SAS/SHARE for Integration with LabKey Server
Configure Webapp Memory
Set Up Robots.txt and Sitemaps
GROUP_CONCAT Install
Example Setups and Configurations
Set up a JMS-Controlled Remote Pipeline Server
Example Installation of Flow Cytometry on Mac OSX
Configure R on Linux
Configure the Virtual Frame Buffer on Linux
Example Linux Installation
DEPRECATED: Install LabKey Server (Linux Installer)
Upgrade LabKey
Manual Upgrade Checklist
Manual Upgrade Script for MacOSX, Solaris and Unsupported Linux Distributions
DEPRECATED: Upgrade LabKey via the Linux Installer
Upgrade Support Policy
Backup and Maintenance
Backup Checklist
A Sample Backup Plan
Sample Scripts for Backup Scenarios
PostgreSQL Maintenance
Administer the Site Down Servlet
Staging, Test and Production Servers
Example of a Large-Scale Installation
Tips for Configuring a Staging Server
Collaboration
Collaboration Tutorial
Step 1: Use the Message Board
Step 2: Collaborate Using a Wiki
Step 3: Track Issues
File Repository Tutorial
Step 1: Set Up a File Repository
Step 2: File Repository Administration
Step 3: Search the Repository
Step 4: Import Data from the Repository
Step 5: Advanced Search and Keywords (Optional)
Files
Upload Files
Upload Files: WebDAV
Share and View Files
Import Data from Files
File Administrator Guide
Files Web Part Administration
Set Site-Wide and Project-Level File Roots
Troubleshoot File Roots and Pipeline Overrides
File Terminology
Integrating S3 Cloud Data Storage
Data Processing Pipeline
Set a Pipeline Override
Enterprise Pipeline
Install Prerequisites for the Enterprise Pipeline
JMS Queue
Globus GRAM Server
RAW to mzXML Converters
Configure LabKey Server to use the Enterprise Pipeline
Configure the Conversion Service
Configure Remote Pipeline Server
Configure Pipeline Path Mapping
Use the Enterprise Pipeline
Create a New Globus GRAM user
Troubleshoot the Enterprise Pipeline
Messages
Use Message Boards
Administer Message Boards
Wikis
Wiki Admin Guide
Copy Wiki Pages
Wiki User Guide
Wiki Syntax
Wiki Syntax: Macros
Special Wiki Pages
Embed Live Content in Wiki Pages or Messages
Examples: Embedded Web Parts
Search Documentation
Add Screenshots to a Wiki
Manage Wiki Attachment List
Wiki: Discussion Link
Issue/Bug Tracking
Using the Issue Tracker
Administering the Issue Tracker
Surveys
Survey Designer: Basics
Survey Designer: Customization
Survey Designer: Reference
Survey Designer: Example Questions
REDCap Survey Data Integration
Contacts
Data and Views
Data Analysis Tutorial
Step 1: Import Data to the Database
Step 2: Sort and Filter Data
Step 3: Visualize Data Trends
Step 4: Integrate Data with a Lookup Column
Step 5: Create an R View (Optional)
Build User Interface
Add Web Parts
Manage Web Parts
Web Part Inventory
Use Tabs
Add Custom Menus
Web Part Configuration Properties
Web Parts: Permissions Required to View
Data Grids
Data Grids: Basics
Sort Data
Filter Data
Select Rows
Customize Views
Saved Filters and Sorts
Join Columns from Multiple Tables
Set Up Lookup Columns
Export Data
Participant Views
Filter by Folder
Field Properties Reference
URL Field Property
Conditional Formats
Date & Number Display Formats
Date and Number Formats Reference
Reports, Views, and Charts
Display a Report or View
Data Views Browser
Manage Reports and Views
Manage Categories
Manage Thumbnail Images
Attachment Reports
Box Plots
Link Reports
Participant Reports
Query Report
Query Snapshot
Quick Charts
R Reports
R View Builder
Saved R Views
Datasets in R
Multi-Panel R Plots
Lattice Plots
Participant Charts in R
R Reports with knitr
Input/Output Substitutions Reference
FAQs for LabKey R Views
R Tutorial Video
Scatter Plots
Time Charts
Why Is a Column Not Available for Charting?
Legacy Reports
Advanced Views / External Reports
Chart Views
Crosstab Views
SQL Queries
LabKey SQL Tutorial
SQL Query Browser
LabKey SQL Reference
Lookups: SQL Syntax
Create a SQL Query
Edit SQL Query Source
Query Metadata
Edit Query Properties
Display a Query
Add a Calculated Column to a Query
Create a Pivot Query
SQL Examples: JOIN, Calculated Columns, GROUP BY
Cross-Folder Queries
External Schemas and Data Sources
External MySQL Data Sources
External Oracle Data Sources
External Microsoft SQL Server Data Sources
External PostgreSQL Data Sources
External SAS Data Sources
Linked Schemas and Tables
Manage Remote Connections
LabKey Data Structures
Choose a Data Storage Type
Preparing Data for Import
Lists
Advanced List Tutorial
Advanced List Tutorial: Set Up
Create a Joined View to Investigate Results
Add a URL Property
Create and Populate Lists
Import Data to a List
Create a List by Defining Fields
Populate a List
Import a List Archive
Manage Lists
Connect Lists
Edit a List Design
Choose a Primary Key
Search
Search Administration
Natural Language Processing Pipeline (NLP)
Configure Natural Language Processing
Process Files Using Natural Language Processing
Instrument Data
Tutorial: Design a General Purpose Assay
Assay Tutorial Set Up
Infer an Assay Design from Spreadsheet Data
Import Assay Data
Configure Data Validation
Work with Assay Data
Integrate Assay Data into a Study
ELISA Assay Tutorial
ELISpot Assay
ELISpot Assay Tutorial
Import ELISpot Data
Review ELISpot Data
ELISpot Properties
FluoroSpot Assay
NAb (Neutralizing Antibody) Assays
NAb Assay Tutorial
Create a NAb Assay Design
Import NAb Assay Data
View High-Throughput NAb Data
Explore NAb Graph Options
Use NAb Data Identifiers
Work with Low-Throughput NAb Data
Work with Multiple Viruses per Plate
NAb Plate File Formats
Customize NAb Plate Template
NAb Properties
Luminex
Luminex® Assay Tutorial Level I
Setup Luminex® Tutorial Project
Create a New Luminex® Assay Design
Import Luminex® Run Data
Exclude Analytes for QC
Import Multi-File Runs
Copy Luminex® Data to Study
Luminex® Assay Tutorial Level II
Import Lists and Assay Archives
Configure R, Packages and Script
Import Luminex® Runs
View 4pl and 5pl Curve Fits
Track Analyte Quality Over Time
Use Guide Sets to Show Expected Ranges
Compare Standard Curves Across Runs
Track Single-Point Controls in Levey-Jennings Plots
Luminex® Reference
Review Luminex® Assay Design
Luminex® Properties
Luminex® file formats
Import Luminex Runs
Review Well Roles
Luminex Calculations
Luminex Conversions
Luminex QC Reports and Flags
Customize Luminex Assay for Script
Review Fields for Script
Troubleshoot Luminex® Transform Scripts and Curve Fit Results
Flow Cytometry
LabKey Flow Module
Supported FlowJo Versions
Flow Cytometry Overview
Tutorial: Import a Flow Workspace
Set up a Flow Folder
Upload Files to Server
Import a Flow Workspace and Analysis
FCS File Resolution
Customize Your View
Examine Graphs
Examine Well Details
Finalize a Dataset View and Export
Tutorial: Perform a LabKey Analysis
Define a Compensation Calculation
Define an Analysis
Apply a Script
View Results
Add Sample Descriptions
Custom Flow Queries
Add Statistics to FCS Queries
Calculate Suites of Statistics for Every Well
Flow Module Schema
Analysis Archive Format
FCS Express
Tutorial: Import Flow Data from FCS Express
Reagent Inventory
FCS keyword utility
Flow Team Members
Microarray
Microarray Assay Tutorial
Expression Matrix Assay Tutorial
Microarray Properties
Proteomics
Proteomics Tutorial
Set Up for Proteomics Analysis
Search mzXML Files
View PeptideProphet Results
View ProteinProphet Results
Compare Runs
Search for a Specific Protein
Proteomics Video
Get Started With LabKey Proteomics
Explore the MS2 Dashboard
Search MS2 Data Via the Pipeline
Set Up MS2 Search Engines
Set Up Mascot
Set Up Sequest
Set Up Comet
Working with mzML files
Set the LabKey Pipeline Root
Search and Process MS2 Data
Configure Common Parameters
Configure X! Tandem Parameters
Configure Mascot Parameters
Configure Sequest Parameters
Sequest Parameters
MzXML2Search Parameters
Examples of Commonly Modified Parameters
Configure Comet Parameters
Import Existing Analysis Results
Launch MS2 pipeline jobs when files are available
Change the versions of the proteomics search tools used by the pipeline
Work with MS2 Runs
View an MS2 Run
Customize Display Columns
Peptide Columns
Protein Columns
View Peptide Spectra
View Protein Details
View Gene Ontology Information
Compare MS2 Runs
Compare ProteinProphet
Export MS2 Runs
Export Spectra Libraries
View, Filter and Export All MS2 Runs
Protein Search
Peptide Search
Loading Public Protein Annotation Files
Using Custom Protein Annotations
Using ProteinProphet
Using Quantitation Tools
Experimental Annotations for MS2 Runs
Protein Expression Matrix Assay
Link Protein Expression Data with Annotations
Exploratory Features
Spectra Counts
Label-Free Quantitation
MS1
MS1 Pipelines
Panorama - Targeted Proteomics
Configure Panorama Folder
Panorama Quality Control
Proteomics Team
Genotyping Workflows
Set Up a Genotyping Dashboard
Example Workflow: LabKey and Galaxy
Example Workflow: LabKey and Illumina
Example Workflow: O'Connor Module
Import Haplotype Assignment Data
Work with Haplotype Assay Data
Illumina Properties
Assay Administrator Guide
Set Up Folder For Assays
Assay Designs and Types
Import Assay Design
Design a New Assay
General Properties
Design a Plate-Based Assay
Edit Plate Templates
Participant/Visit Resolver
Manage an Assay Design
Improve Data Entry Consistency & Accuracy
Set up a Data Transformation Script
Integrate Assay Data into a Study
Copy-To-Study History
Experiment Descriptions & Archives (XARs)
Experiment Terminology
Samples and Sample Sets
Run Groups
XAR File Tutorial
Uses of XAR.xml Files
Import a XAR.xml
Troubleshoot XAR Import
Import XAR Files Using the Data Pipeline
Example 1: Review a Basic XAR.xml
Examples 2 & 3: Describe Protocols
Examples 4, 5 & 6: Describe LCMS2 Experiments
Design Goals and Directions
Life Science Identifiers (LSIDs)
LSID Substitution Templates
Assay User Guide
Import Assay Runs
Electronic Laboratory Notebooks (ELN)
Studies
Study Tour
Tutorial: Cohort Studies
Step 1: Install the Sample Study
Step 2: Study Data Dashboards
Step 3: Integrate Data from Different Sources
Step 4: Compare Participant Performance
Tutorial: Set Up a New Study
Step 1: Define Study Properties
Step 2: Import Datasets
Step 3: Assign Cohorts
Step 4: Import Specimens
Step 5: Enable Comments
Study User Guide
Study Navigation
The Study Navigator
Study Data Browser
Cohorts
Participant Groups
Comments
Dataset Quality Control States
Study Administrator Guide
Create a Study
Create and Populate Datasets
Create a Dataset from a File
Create a Dataset by Defining Fields
Create Multiple Datasets from schema.TSV
Import Data to a Dataset
Import Through the Files Web Part
Import via Copy/Paste
Import From a Dataset Archive
Create Pipeline Configuration File
Import Study Data From REDCap Projects
Edit Dataset Properties
Dataset Fields Reference
Pre-Defined Fields
Dataset Properties Reference
Use Visits or Timepoints
Create Visits
Edit Visits or Timepoints
Import Visit Map
Import Visit Names / Aliases
Manage a Study
Custom Study Properties
Manage Datasets
Manage Visits or Timepoints
Study Schedule
Manage Locations
Manage Cohorts
Manage Participant IDs
Alternate Participant IDs
Alias Participant IDs
Manage Comments
Manage Study Security (Dataset-Level Security)
Configure Permissions for Reports & Views
Matrix of Permissions
Securing Portions of a Dataset (Row and Column Level Security)
Manage Dataset QC States
Manage Study Products
Manage Treatments
Manage Assay Schedule
Demonstration Mode
Create a Vaccine Study Design
Import, Export, and Reload a Study
Export Study Objects
Study Import/Export Files and Formats
Serialized Elements and Attributes of Lists and Datasets
Publish a Study
Publish a Study: Protected Health Information
Publish a Study: Refresh Snapshots
Ancillary Studies
Shared Datasets and Timepoints
Specimens
Specimen Request Tutorial
Specimen Tutorial: Repository Set Up (Admin)
Specimen Tutorial: Request System (Coordinator)
Specimen Tutorial: Request Specimens (User)
Specimen Tutorial: Track Requests (Coordinator)
Specimen Administrator Guide
Import Specimen Spreadsheet Data
Import a Specimen Archive
Specimen Archive File Reference
Specimen Archive Data Destinations
Troubleshoot Specimen Import
Import FreezerPro Data
Specimen Properties and Rollup Rules
Customize Specimens Web Part
Flag Specimens for Quality Control
Edit Specimen Data
Customize the Specimen Request Email Template
Export a Specimen Archive
Specimen Coordinator Guide
Email Specimen Lists
View Specimen Data
Generate Specimen Reports
Development
LabKey Client APIs
JavaScript API
Tutorial: Create Applications with the JavaScript API
User Interface: Request Form
Confirmation Page
R Histogram (Optional)
Summary Report For Managers
Repackaging the App as a Module
Tutorial: Use URLs to Filter and Pass Data
Choose Parameters
Show Filtered Grid
Tutorial Video: Building Reports and Custom User Interfaces
JavaScript API - Samples
JavaScript Views
Export Data Grid as a Script
Export Chart as JavaScript
Custom HTML/JavaScript Participant View
Custom Button Bars
Insert into Audit Table via API
Declare Script Dependencies
Loading ExtJS On Each Page
Licensing for the ExtJS API
Search API Documentation
Naming & Documenting JavaScript APIs
Naming Conventions for JavaScript APIs
How to Generate JSDoc
JsDoc Annotation Guidelines
Java API
Prototype LabKey JDBC Driver
Perl API
Python API
Tutorial: Python API
Set up the Python API
Use the Python API
Rlabkey Package
Troubleshooting Rlabkey Connections
SAS Macros
SAS Setup
SAS Macros
SAS Security
SAS Demos
HTTP Interface
Examples: Controller Actions
Example: Access APIs from Perl
Develop Modules
Map of Module Files
Example Modules
Modules: Queries, Views and Reports
Module Directories Setup
Module Query Views
Module SQL Queries
Module-Based Queries: Metadata
Module R Reports
Module-Based Reports: Metadata
Module HTML and Web Parts
Module Database Transition Scripts
Modules: Assay Types
Tutorial: Define an Assay Type in a Module
Assay Custom Domains
Assay Custom Views
Example Assay JavaScript Objects
Assay Query Metadata
Customize Batch Save Behavior
SQL Scripts for Module-Based Assays
Transformation Scripts
Example Workflow: Develop a Transformation Script (perl)
Example Transformation Scripts (perl)
Transformation Scripts in R
Transformation Scripts in Java
Transformation Scripts for Module-based Assays
Run Properties Reference
Transformation Script Substitution Syntax
Modules: ETLs
Tutorial: Extract-Transform-Load (ETL)
ETL Tutorial: Set Up
ETL Tutorial: Create a New ETL
ETL: User Interface
ETL: Schedules and Options
ETL: Stored Procedures
ETL: Stored Procedures in MS SQL Server
ETL: Functions in PostgreSQL
ETL: SQL Scripts
ETL: Logs and Error Handling
ETL: Remote Connections
ETL Examples
ETL Reference
Modules: Java
Module Architecture
Getting Started with the Demo Module
Creating a New Java Module
The LabKey Server Container
Implementing Actions and Views
Implementing API Actions
Integrating with the Pipeline Module
Integrating with the Experiment Module
Using SQL in Java Modules
GWT Integration
GWT Remote Services
Java Testing Tips
HotSwapping Java classes
Deprecated Components
Modules: Folder Types
Modules: SQL Scripts
Deploy Modules to a Production Server
Reloading Modules
Upgrade Modules
MiniProfiler
Main Credits Page
Module Properties Reference
Common Development Tasks
Trigger Scripts
Script Pipeline: Running R and Other Scripts in Sequence
LabKey URLs
URL Actions
How To Find schemaName, queryName & viewName
LabKey Keys
LabKey/Rserve Setup Guide
Reference Resources with Context Paths
Web Application Security
HTML Encoding
Cross-Site Request Forgery (CSRF) Protection
LabKey Open Source Project
Source Code
Release Schedule
Issue Tracker
LabKey Scrum FAQ
Developer Email List
Branch Policy
Test Procedures
Running Automated Tests
Hotfix Policy
Feature Owners
Previous Releases
Previous Releases -- Details
Submit Contributions
Confidential Data
CSS Design Guidelines
UI Design Patterns
Design Guidelines Supplemental
Documentation Style Guide
Check in to the Source Project
Renaming files in Subversion
Set up a Development Machine
Enlisting in the Version Control Project
Enlisting Proteomics Binaries
Customizing the Build
Machine Security
Notes on Setting up a Mac for LabKey Development
Building with JDK 8
Developer Reference
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