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LabKey Server
Assay Data
Mass Spectrometry
Discovery Proteomics
Work with MS2 Data
Documentation: Version 19.3
Work with MS2 Data
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The following topics cover different aspects of working with MS2 data:
Search MS2 Data Via the Pipeline
: Upload MS2 data for analysis, performing processing steps at the same time.
configMs2search
: Select specific search engine.
Search and Process MS2 Data
: Configure parameters.
Import Existing Analysis Results
Trigger MS2 Processing Automatically
Set Proteomics Search Tools Version
Explore the MS2 Dashboard
View an MS2 Run
Compare MS2 Runs
Export MS2 Runs
View, Filter and Export All MS2 Runs
Related Topics
Discovery Proteomics Tutorial
: Explore the basics using sample data in our tutorial.
Run Groups
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Documentation Home
What's New in 19.3
Release Notes 19.3
Upcoming Features
Getting Started
Try it Now: Data Grids
Trial Servers
Explore LabKey Server - Hosted Trial
Introduction to LabKey Server: Trial
Exploring LabKey Collaboration
Exploring Laboratory Data
Exploring LabKey Studies
Exploring LabKey Security
Exploring Project Creation
Extending Your Trial
Trial Server: Modules
LabKey Server - Hosted Trial
Explore LabKey Biologics - Hosted Trial
Learn About LabKey Biologics: Trial
Virtual Machine Server - On-Premise Evaluation
Install LabKey for Evaluation
Tutorials
Set Up for Tutorials: Trial
Set Up for Tutorials - Non-Trial
Navigation and UI Basics
LabKey Server Editions
Training
LabKey Support Portal Pages
Modules in LabKey Server Editions
LabKey Server
Introduction to LabKey Server
Navigate Server
Data Basics
LabKey Data Structures
Where Should My Data Go?
Field Editor
Preparing Data for Import
Data Grids
Data Grids: Basics
Import Data
Sort Data
Filter Data
Filtering Expressions
Saved Filters and Sorts
Column Summary Statistics
Select Rows
Customize Grid Views
Export Data Grid
Join Columns from Multiple Tables
Lookup Columns
Participant Details View
Query Scope: Filter by Folder
Field Properties Reference
URL Field Property
String Expression Format Functions
Conditional Formats
Date & Number Display Formats
Date and Number Formats Reference
Reports and Charts
Report Web Part: Display a Report or Chart
Data Views Browser
Query Snapshots
Attachment Reports
Link Reports
Participant Reports
Query Report
Manage Data Views
Manage Dataset/Report Notifications
Manage Categories
Manage Thumbnail Images
Measure and Dimension Columns
Legacy Reports
Advanced Reports / External Reports
Legacy Chart Views
Crosstab Reports
Visualizations
Bar Charts
Box Plots
Line Plots
Pie Charts
Scatter Plots
Time Charts
Column Visualizations
Quick Charts
Integrate with Tableau
Lists
Tutorial: Lists
Step 1: Set Up List Tutorial
Step 2: Create a Joined Grid
Step 3: Add a URL Property
Create Lists
Create a List Design
Import a List Archive
Choose a Primary Key
Edit a List Design
Populate a List
Manage Lists
Connect Lists
R Reports
R Report Builder
Saved R Reports
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 Reports
RStudio Integration
RStudio Set Up - Linux and OSX Systems
Docker and TLS Set Up
Connect to RStudio Pro
Set Up RStudio Pro
Edit R Reports in RStudio
Export Data to RStudio
Advanced Initialization of RStudio
Configure Docker Host
SQL Queries
LabKey SQL Tutorial
SQL Query Browser
Create a SQL Query
Edit SQL Query Source
LabKey SQL Reference
Lookups: SQL Syntax
LabKey SQL Utility Functions
Query Metadata
Query Metadata: Examples
Edit Query Properties
Query Web Part
SQL Synonyms
LabKey SQL Examples
Calculated Columns
Pivot Queries
Queries Across Folders
Join Queries Across Schema
Parameterized SQL Queries
Various LabKey SQL Examples
Premium Resource: Bulk Editing
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
External Redshift Data Sources
Linked Schemas and Tables
Manage Remote Connections
Controlling Data Scope
Data Quality Control
Quality Control Trend Reports
Define QC Trend Report
Use QC Trend Reports
QC Trend Report Guide Sets
Search
Search Administration
Spotfire Integration
Premium Resource: Embed Spotfire Visualizations
LabKey Natural Language Processing (NLP)
Natural Language Processing (NLP) Pipeline
Metadata JSON Files
Document Abstraction Workflow
Automatic Assignment for Abstraction
Manual Assignment for Abstraction
Abstraction Task Lists
Document Abstraction
Review Document Abstraction
Review Multiple Result Sets
NLP Result Transfer
Configure LabKey NLP
Run NLP Pipeline
Assay Data
Tutorial: Design a General Purpose Assay Type (GPAT)
Step 1: Assay Tutorial Setup
Step 2: Infer an Assay Design from Spreadsheet Data
Step 3: Import Assay Data
Step 4: Work with Assay Data
Step 5: Data Validation
Step 6: Integrate Assay Data into a Study
Tutorial: ELISA Assay
ELISpot Assay
Tutorial: ELISpot Assay Tutorial
Import ELISpot Data
Review ELISpot Data
ELISpot Properties
Flow Cytometry
Flow Cytometry Overview
LabKey Flow Module
Set Up a Flow Folder
Tutorial: Import a Flow Workspace
Step 1: Customize Your Grid View
Step 2: Examine Graphs
Step 3: Examine Well Details
Step 4: Export Flow Data
Step 5: Flow Quality Control
Tutorial: Set Flow Background
Tutorial: Perform a LabKey Flow Analysis
Set Up Flow For LabKey Analysis
Step 1: Define a Compensation Calculation
Step 2: Define an Analysis
Step 3: Apply a Script
Step 4: View Results
Import a Flow Workspace and Analysis
FCS File Resolution
Edit Keywords
Add Sample Descriptions
Custom Flow Queries
Add Statistics to FCS Queries
Calculate Suites of Statistics for Every Well
Flow Module Schema
Analysis Archive Format
Supported FlowJo Versions
FCS Express
Tutorial: Import Flow Data from FCS Express
Add Flow Data to a Study
FCS keyword utility
Flow Team Members
FluoroSpot Assay
HPLC - High-Performance Liquid Chromatography
Luminex
Luminex Assay Tutorial Level I
Set Up Luminex Tutorial Folder
Step 1: Create a New Luminex Assay Design
Step 2: Import Luminex Run Data
Step 3: Exclude Analytes for QC
Step 4: Import Multi-File Runs
Step 5: Copy Luminex Data to Study
Luminex Assay Tutorial Level II
Step 1: Import Lists and Assay Archives
Step 2: Configure R, Packages and Script
Step 3: Import Luminex Runs
Step 4: View 4pl and 5pl Curve Fits
Step 5: Track Analyte Quality Over Time
Step 6: Use Guide Sets for QC
Step 7: Compare Standard Curves Across Runs
Track Single-Point Controls in Levey-Jennings Plots
Import Luminex Runs
Luminex Calculations
Luminex QC Reports and Flags
Luminex Reference
Review Luminex Assay Design
Luminex Properties
Luminex File Formats
Review Well Roles
Luminex Conversions
Customize Luminex Assay for Script
Review Fields for Script
Troubleshoot Luminex Transform Scripts and Curve Fit Results
Microarray: Expression Matrix
Expression Matrix Assay Tutorial
Mass Spectrometry
Panorama - Targeted Mass Spectrometry
Panorama Partners Program
Configure Panorama Folder
Panorama Data Import
Panorama Document Revision Tracking
Panorama: Skyline Replicates and Lists
Skyline Annotation Data
Skyline Audit Log
Panorama: Calibration Curves
Panorama: Figures of Merit and Pharmacokinetics (PK)
Panorama QC Dashboard
Panorama QC Plots
Panorama QC Plot Types
Panorama QC Annotations
Panorama QC Guide Sets
Panorama: Pareto Plots
Panorama: Heat Maps
Panorama Premium: Configure QC Metrics
Panorama Premium: Outlier Notifications
Working with Small Molecule Targets
Discovery Proteomics
Discovery Proteomics Tutorial
Step 1: Set Up for Proteomics Analysis
Step 2: Search mzXML Files
Step 3: View PeptideProphet Results
Step 4: View ProteinProphet Results
Step 5: Compare Runs
Step 6: Search for a Specific Protein
Work with MS2 Data
Search MS2 Data Via the Pipeline
Set Up MS2 Search Engines
Set Up Mascot
Set Up Sequest
Set Up Comet
Working with mzML Files
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
Trigger MS2 Processing Automatically
Set Proteomics Search Tools Version
Explore the MS2 Dashboard
View an MS2 Run
Customize Display Columns
Peptide Columns
Protein Columns
View Peptide Spectra
View Protein Details
View Gene Ontology Information
Experimental Annotations for MS2 Runs
Protein Search
Peptide Search
Compare MS2 Runs
Compare ProteinProphet
Export MS2 Runs
Export Spectra Libraries
View, Filter and Export All MS2 Runs
Work with Mascot Runs
Discovery Proteomics Video
Loading Public Protein Annotation Files
Using Custom Protein Annotations
Using ProteinProphet
Using Quantitation Tools
MaxQuant Module
Link Protein Expression Data with Annotations
Spectra Counts
Label-Free Quantitation
Combine XTandem Results
Run Groups
Protein Expression Matrix Assay
Proteomics Team
NAb (Neutralizing Antibody) Assays
Tutorial: NAb Assay
Step 1: Create a NAb Assay Design
Step 2: Import NAb Assay Data
Step 3: View High-Throughput NAb Data
Step 4: Explore NAb Graph Options
Work with Low-Throughput NAb Data
Use NAb Data Identifiers
NAb Assay QC
Work with Multiple Viruses per Plate
NAb Plate File Formats
Customize NAb Plate Template
NAb Properties
Signal Data Assay
Assay Administrator Guide
Assay Feature Matrix
Set Up Folder For Assays
Assay Designs and Types
Export/Import Assay Design
Design a New Assay
Editing Assay Data
Assay Design Properties
Design a Plate-Based Assay
Edit Plate Templates
Participant/Visit Resolver Field
Manage an Assay Design
Assay QC States - Admin Guide
Improve Data Entry Consistency & Accuracy
Set up a Data Transformation Script
Copy Assay Data into a Study
Copy-To-Study History
XAR Archives
XAR Terminology
XAR Files
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
Life Science Identifiers (LSIDs)
LSID Substitution Templates
Assay User Guide
Import Assay Runs
Multi-File Assay Runs
Assay QC States - User Guide
Exclude Assay Data
Reimport Assay Runs
Export Assay Data
Assay Request Tracker
Premium Resource: Using the Assay Request Tracker
Premium Resource: Assay Request Tracker Administration
Electronic Laboratory Notebooks (ELN)
Tutorial: Electronic Lab Notebook
Step 1: Create the User Interface
Step 2: Import Lab Data
Step 3: Create a Lookup from Assay Data to Samples
Step 4: Using and Extending the ELN
Reagent Inventory
Data Classes
Sample Sets
Create Sample Set
Samples: Generate Unique IDs
Import to Sample Sets
View SampleSets and Samples
Link Assay Data to Sample Sets
Parent Samples: Derivation and Lineage
Sample Sets: Examples
Longitudinal Studies
Study Tour
Tutorial: Longitudinal Studies
Step 1: Install the Tutorial 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: Create Study Framework
Step 2: Add Participants and Data
Step 3: Identify Cohorts
Step 4: Integrate and Visualize Data
Step 5: Add Specimen Data
Study User Guide
Study Navigation
Study Data Browser
Cohorts
Participant Groups
Comments
Dataset QC States - User Guide
Study Administrator Guide
Study Management
Additional 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
Securing Portions of a Dataset (Row and Column Level Security)
Dataset QC States - Admin Guide
Manage Study Products
Manage Treatments
Manage Assay Schedule
Assay Progress Report
Demonstration Mode
Create a Study
Create and Populate Datasets
Create a Dataset from a File
Create a Dataset by Defining Fields
Tutorial: Inferring Datasets from Excel and TSV Files
Import Data to a Dataset
Import via Copy/Paste
Import From a Dataset Archive
Create Pipeline Configuration File
Import Study Data From REDCap Projects
Dataset Properties
Study: Reserved and Special Fields
Edit Dataset Properties
Dataset System Fields
Visits and Dates
Create Visits Manually
Edit Visits or Timepoints
Import Visit Map
Import Visit Names / Aliases
Continuous Studies
Study Visits and Timepoints FAQ
Import, Export, and Reload a Study
Export a Study
Import a Study
Reload a Study
Study Archive Files and Formats
Serialized Elements and Attributes of Lists and Datasets
Publish a Study
Publish a Study: Protected Health Information / PHI
Publish a Study: Refresh Snapshots
Ancillary Studies
Shared Datasets and Timepoints
Data Aliasing
Study Data Model
How is Study Data Stored in LabKey Server?
Create a Vaccine Study Design
Vaccine Study: Data Storage
Specimen Tracking
Tutorial: Specimen Request System
Step 1: Repository Setup (Admin)
Step 2: Request System (Specimen Coordinator)
Step 3: Request Specimens (User)
Step 4: Track Requests (Specimen Coordinator)
Specimens: Administrator Guide
Import Specimen Spreadsheet Data
Import a Specimen Archive
Specimen Archive File Reference
Specimen Archive Data Destinations
Troubleshoot Specimen Import
Import FreezerPro Data
Delete Specimens
Specimen Properties and Rollup Rules
Customize Specimens Web Part and Grid Views
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 Vials and Grouped Vials
Generate Specimen Reports
Laboratory Information Management System (LIMS)
Using Sample Sets as an Alternative to a Specimen Repository
Electronic Health Records (EHR)
Premium Resource: EHR: Animal History
Premium Resource: EHR: Animal Search
Premium Resource: EHR: Data Entry
Premium Resource: EHR: Genetics Algorithms
Premium Resource: EHR: Administration
Premium Resource: EHR: Billing Module
Premium Resource: EHR: Define Billing Rates and Fees
Premium Resource: EHR: Preview Billing Reports
Premium Resource: EHR: Perform Billing Run
Premium Resource: EHR: Historical Billing Data
EHR Team
EHR Project Setup
Structured Narrative Datasets
SND: Packages
SND: Categories
SND: Super-packages
SND: Projects
SND: Events
SND: QC and Security
SND: APIs
SND: Event Triggers
SND: UI
Extending SND Tables
XML Import of Packages
Enterprise Master Patient Index Integration
Collaboration
Tutorial: Collaboration Tools
Step 1: Configure a Message Board
Step 2: Create a Wiki
Step 3: Track Issues
Tutorial: File Repository
Step 1: Set Up a File Repository
Step 2: File Repository Administration
Step 3: Search the Repository
Step 4: Import Data from the Repository
Files
Using the Files Repository
Share and View Files
Controlling File Display via the URL
Import Data from Files
Linking Assays with Images and Other Files
Linking Data Records with External Files
File Metadata
File Transfer Module / Globus File Sharing
File Administrator Guide
Files Web Part Administration
Upload Files: WebDAV
Set File Roots
Troubleshoot File Roots and Pipeline Overrides
File Terminology
Integrating S3 Cloud Data Storage
Enterprise Pipeline
Install Prerequisites for the Enterprise Pipeline
JMS Queue
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
Troubleshoot the Enterprise Pipeline
Messages
Use Message Boards
Administer Message Boards
Object-Level Discussions
Wikis
Wiki Admin Guide
Copy Wiki Pages
Wiki User Guide
Wiki Syntax
Wiki Syntax: Macros
Markdown Syntax
Special Wiki Pages
Embed Live Content in HTML Pages or Messages
Examples: Embedded Web Parts
Web Part Configuration Properties
Add Screenshots to a Wiki
Manage Wiki Attachment List
Issue/Bug Tracking
Using the Issue Tracker
Issue Tracker: Administration
Electronic Data Capture (EDC)
Tutorial: Survey Designer, Step 1
Tutorial: Survey Customization, Step 2
Survey Designer: Reference
Survey Designer: Examples
REDCap Survey Data Integration
Medidata / CDISC ODM Integration
Workflow Module
Workflow Tutorial
Step 1: Set Up Workflow Tutorial
Step 2: Run Example Workflow Process
Step 3: Workflow Process Definition
Step 4: Customize Workflow Process Definition
Workflow Process Definition
Adjudication Module
Set Up an Adjudication Folder
Initiate an Adjudication Case
Make an Adjudication Determination
Monitor Adjudication
Infection Monitor
Audit of Adjudication Events
Role Guide: Adjudicator
Role Guide: Adjudication Lab Personnel
Tours for New Users (Deprecated)
Hopscotch Options for Tours (Deprecated)
Contacts
How to Cite LabKey Server
Development
Set Up a Development Machine
Access the Source Code
Add the Proteomics Binaries
Gradle Build Overview
Build LabKey from Source
Customize the Build
Node.js Build Dependency
SVN and Git Ignore Configurations
Build Offline
Gradle Cleaning
Gradle Properties
Gradle: How to Add Modules
Gradle: Declare Dependencies
Gradle Tips and Tricks
Run Selenium Tests
Create Production Builds
Machine Security
Notes on Setting up OSX for LabKey Development
Tomcat 7 Encoding
Troubleshoot Development Machines
Premium Resource: IntelliJ Reference
LabKey Client APIs
JavaScript API
Tutorial: Create Applications with the JavaScript API
Step 1: Create Request Form
Step 2: Confirmation Page
Step 3: R Histogram (Optional)
Step 4: Summary Report For Managers
Repackaging the App as a Module
Tutorial: Use URLs to Pass Data and Filter Grids
Choose Parameters
Show Filtered Grid
Tutorial: Visualizations in JavaScript
Step 1: Export Chart as JavaScript
Step 2: Embed the Script in a Wiki
Modify the Exported Chart Script
Display the Chart with Minimal UI
JavaScript API - Examples
Adding a Report to a Data Grid with JavaScript
Export Data Grid as a Script
Custom HTML/JavaScript Participant Details View
Example: Master-Detail Pages
Custom Button Bars
Premium Resource: Invoke JavaScript from Custom Buttons
Premium Resource: Sample Status Demo
Insert into Audit Table via API
Programming the File Repository
Vocabulary Domains
Declare 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
LabKey JDBC Driver
Remote Login API
Security Bulk Update via API
Perl API
Python API
Premium Resource: Python API Demo
Rlabkey Package
Troubleshoot Rlabkey
Premium Resource: Example Code for QC Reporting
SAS Macros
SAS Setup
SAS Macros
SAS Security
SAS Demos
HTTP Interface
Examples: Controller Actions / API Test Page
Example: Access APIs from Perl
External ODBC Connections
ODBC Data Sources and SQL Server Reporting Service (SSRS)
Secure ODBC Connections
API Keys
Compliant Access via Session Key
Develop Modules
Premium Resource: Migrate Module from SVN to GitHub
Tutorial: Hello World Module
Map of Module Files
Example Modules
Modules: Queries, Views and Reports
Module Directories Setup
Module Query Views
Module SQL Queries
Module R Reports
Module HTML and Web Parts
Modules: JavaScript Libraries
Modules: Assay Types
Assay Custom Domains
Assay Custom Details View
Loading 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
Premium Resource: Python Transformation Script
Premium Resource: Create Samples with Transformation Script
Run Properties Reference
Transformation Script Substitution Syntax
Warnings in Transformation Scripts
Modules: Folder Types
Modules: Query Metadata
Modules: Report Metadata
Modules: Custom Header
Modules: Custom Banner
Modules: Custom Footer
Modules: SQL Scripts
Modules: Database Transition Scripts
Modules: Domain Templates
Modules: Java
Module Architecture
Getting Started with the Demo Module
Tutorial: Hello World Java Module
The LabKey Server Container
Implementing Actions and Views
Implementing API Actions
Integrating with the Pipeline Module
Integrating with the Experiment API
Using SQL in Java Modules
GWT Integration
GWT Remote Services
Database Development Guide
Java Testing Tips
HotSwapping Java classes
Modules: Custom Login Pages
ETL: Extract Transform Load
Tutorial: Extract-Transform-Load (ETL)
ETL Tutorial: Set Up
ETL Tutorial: Run an ETL Process
ETL Tutorial: Create a New ETL Process
ETL: Define an ETL Using XML
ETL: User Interface
ETL: Configuration and Schedules
ETL: Filter Strategies
ETL: Column Mapping
ETL: Queuing ETL Processes
ETL: Stored Procedures
ETL: Stored Procedures in MS SQL Server
ETL: Functions in PostgreSQL
ETL: Check For Work From a Stored Procedure
ETL: SQL Scripts
ETL: Remote Connections
ETL: Logs and Error Handling
ETL: All Jobs History
ETL: Examples
ETL: Reference
Premium Resource: ETL Best Practices
Deploy Modules to a Production Server
Upgrade Modules
Main Credits Page
Module Properties Reference
Common Development Tasks
Trigger Scripts
Availability of Server-side Trigger Scripts
Script Pipeline: Running Scripts in Sequence
LabKey URLs
URL Actions
How To Find schemaName, queryName & viewName
LabKey/Rserve Setup Guide
Web Application Security
HTML Encoding
Cross-Site Request Forgery (CSRF) Protection
Profiler Settings
Using loginApi.api
Configuring IntelliJ for XML File Editing
Premium Resource: LabKey Coding Standards and Practices
Premium Resource: Feature Branch Workflow
Premium Resource: Git Branch Naming
Premium Resource: Best Practices for Writing Automated Tests
Premium Resource: ReactJS Development Resources
LabKey Open Source Project
Release Schedule
Premium Resource: Previous Releases
Premium Resource: Previous Release Details
Open Source Project: Entering Issues
Branch Policy
Test Procedures
Run Automated Tests
Hotfix Policy
Submit Contributions
Confidential Data
CSS Design Guidelines
UI Design Patterns
Documentation Style Guide
Check in to the Source Project
Renaming files in Subversion
Developer Reference
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
Project and Folder Basics
Site Structure: Best Practices
Folder Types
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
Establish Terms of Use
Workbooks
Shared Project
Build User Interface
Page Admin Mode
Add Web Parts
Manage Web Parts
Web Part Inventory
Use Tabs
Add Custom Menus
Web Parts: Permissions Required to View
Old/New User Interface Comparison
Security
Configure Permissions
Security Groups
Global Groups
Site Groups
Project Groups
Guests / Anonymous Users
Security Roles Reference
Role / Permissions Matrix
Administrator Role / Permissions Matrix
Matrix of Report, Chart, and Grid Permissions
Developer Roles
User Accounts
My Account
Site Administrator
Add Users
Manage Users
Manage Project Users
Authentication
Configure Database Authentication
Passwords
Password Reset & Security
Configure SAML Authentication
Configure CAS Single Sign On Authentication (SSO)
Configure CAS Identity Provider
Configure LDAP Authentication
LDAP User/Group Synchronization
Configure Duo Two-Factor Authentication
Create a netrc file
HTTP Basic Authentication
Virus Checking
Test Security Settings by Impersonation
Premium Resource: Best Practices for Security Scanning
Compliance
Compliance: Overview
Compliance: Checklist
Compliance: User Accounts and Login
Compliance: Setting PHI Levels on Fields
Compliance: Terms of Use
Compliance: Security Roles
Compliance: Configure PHI Data Handling
Compliance: Logging
Compliance: PHI Report
Electronic Signatures / Sign Data
GDPR Compliance
Premium Resource: Configuring LabKey for GDPR Compliance
Admin Console
Site Settings
Usage/Exception Reporting - Details
Look and Feel Settings
Page Elements
Web Site Theme
Email Template Customization
Experimental Features
Configure Allowable External Redirect Hosts
Manage Missing Value Indicators / Out of Range Values
Short URLs
Configure System Maintenance
Configure Scripting Engines
Audit Site Activity
SQL Query Logging
Export Diagnostic Information
Actions Diagnostics
Cache Statistics
Dump Heap
Memory Usage
Running Threads
Query Performance
Site/Container Validation
Data Processing Pipeline
Set a Pipeline Override
Pipeline Protocols
File Watchers
Create a File Watcher
File Watcher Tasks
File Watchers for Script Pipelines
File Watcher Pattern Options
File Watcher Examples
Install LabKey
Premium Resource: Reference Architecture / System Requirements
Premium Resource: Install LabKey on Linux Systems
Install LabKey Manually
Install Required Components
Configure the LabKey Web Application
labkey.xml Configuration File Reference
Third-Party Components and Licenses (Optional Install)
Creating & Installing SSL/TLS Certificates on Tomcat
Example Hardware/Software Configurations
Common Install Tasks
Install Microsoft SQL Server
Install PostgreSQL (Windows)
Install PostgreSQL (Linux or OSX)
Notes on Installing PostgreSQL on All Platforms
Install and Set Up R
Configure an R Docker Engine
Determine Available Graphing Functions
Configure R on Linux
Install SAS/SHARE for Integration with LabKey Server
Configure Tomcat Webapp Memory
Server Bootstrap Properties
Set Up Robots.txt and Sitemaps
GROUP_CONCAT Install
Sending Email from Non-LabKey Domains
PremiumStats Install
Deploying an AWS Windows Application Firewall
Configure the Virtual Frame Buffer on Linux
Supported Technologies
Troubleshoot Server Installation and Configuration
Installation Error Messages
Dump Memory and Thread Usage Debugging Information
Community Edition Modules - Descriptions
Additional Source Modules
Upgrade LabKey
Manual Upgrade Checklist
Manual Upgrade Script for Linux and OSX
Premium Resource: Upgrade OpenJDK on AWS Ubuntu Servers
Upgrade Support Policy
Backup and Maintenance
Backup Checklist
An Example Backup Plan
Example Scripts for Backup Scenarios
PostgreSQL Maintenance
Post a Site Down Message
Staging, Test and Production Servers
Example of a Large-Scale Installation
Tips for Configuring a Staging Server
Troubleshoot LabKey Server
LabKey Biologics
Introduction to LabKey Biologics
LabKey Biologics - Videos
Biologics Tutorials
Biologics Tutorial: Navigate and Search the Registry
Biologics Tutorial: Add Sequences to the Registry
Biologics Tutorial: Register Samples and Experiments
Biologics Tutorial: Work with Mixtures and Batches
Biologics Tutorial: Create a New Biologics Project
Terminology
Entity Registration
Navigate the Registry
Search the Registry
Register Nucleotide Sequences
Register Protein Sequences
Protein Sequence Annotations
Register Leaders, Linkers, and Tags
Register Molecules
Molecule Sets and Molecular Species
Vectors, Constructs, Cell Lines, and Expression Systems
Entity Lineage
Bulk Registration of Entities
Use the Registry API
Biologics: Samples
Generate Samples
Sample Sets and Detail Pages
Samples and Sample Sets Within LabKey Server
Biologics: Assay Management
Biologics Assay Data
Biologics: Upload Assay Data
Media Registration
Registering Ingredients and Raw Materials
Registering Mixtures (Recipes)
Registering Batches
Biologics: Workflow Management
Biologics Workflow
Biologics: Experiments
Biologics Administration
Biologics Admin: Grids, Detail Views, and Entry Forms
Biologics Admin: Charts and Custom Grids
Biologics Admin: Set Up Assays
Biologics Admin: Assay Grids
Biologics Admin: Service Request Tracker Set Up
Premium Resources
Community Resources
LabKey Terminology/Glossary
FAQ - Frequently Asked Questions
System Integration: Instruments and Software
Demos
Videos
Project Highlight: FDA MyStudies Mobile App
LabKey User Conference Resources
LabKey User Conference 2019
LabKey User Conference 2018
LabKey User Workshop 2018
LabKey User Conference 2017
LabKey User Conference 2016
LabKey User Conference 2015
LabKey User Conference 2014
LabKey User Conference 2013
LabKey User Conference 2012
LabKey User Conference 2011
Collaborative DataSpace: User Guide
DataSpace: Learn About
DataSpace: Find Subjects
DataSpace: Plot Data
DataSpace: View Data Grid
DataSpace: Monoclonal Antibodies
Documentation Archive
Release Notes: 19.2
What's New in 19.2
Release Notes 19.1
What's New in 19.1.x
Release Notes 18.3
What's New in 18.3
What's New in 18.3
Feature Changes
Release Notes 18.2
What's New in 18.2
Upcoming Feature Changes in 18.3
Release Notes 18.1
What's New in 18.1
Release Notes 17.3
Release Notes 17.2
LabKey Privacy Policy
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