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LabKey Server
Assay Data
Mass Spectrometry
Discovery Proteomics
Work with MS2 Data
Documentation
Work with MS2 Data
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The topics in this section cover managing, analyzing, and sharing high volumes of tandem mass spectrometry (MS2) data:
Search MS2 Data Via the Pipeline
: Analyze MS2 data using pipeline protocols.
Set Up MS2 Search Engines
: Select specific search engine.
Search and Process MS2 Data
: Configure parameters.
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
Search
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Project
Current Folder
Current Folder & Subfolders
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Files
Issues
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Subjects
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Documentation Home
What's New in 24.3
Release Notes 24.3 (March 2024)
Upcoming Features
Getting Started
Try it Now: Data Grids
Trial Servers
Explore LabKey Server with a trial in LabKey Cloud
Introduction to LabKey Server: Trial
Exploring LabKey Collaboration
Exploring Laboratory Data
Exploring LabKey Studies
Exploring LabKey Security
Exploring Project Creation
Extending Your Trial
LabKey Server trial in LabKey Cloud
Design Your Own Study
Explore LabKey Biologics with a trial in LabKey Cloud
Learn About LabKey Biologics: Trial
Install LabKey for Evaluation
Tutorials
Set Up for Tutorials: Trial
Set Up for Tutorials: Non-Trial
Navigation and UI Basics
LabKey Server Editions
Training
Modules in LabKey Server Editions
LabKey Server
Introduction to LabKey Server
Navigate the Server
Data Basics
LabKey Data Structures
Preparing Data for Import
Field Editor
Field Types and Properties
Text Choice Fields
URL Field Property
Conditional Formats
String Expression Format Functions
Date & Number Display Formats
Date and Number Formats Reference
Lookup Columns
Protecting PHI Data
Data Grids
Data Grids: Basics
Import Data
Sort Data
Filter Data
Filtering Expressions
Column Summary Statistics
Customize Grid Views
Saved Filters and Sorts
Select Rows
Export Data Grid
Participant Details View
Query Scope: Filter by Folder
Reports and Charts
Jupyter Reports
Report Web Part: Display a Report or Chart
Data Views Browser
Query Snapshots
Attachment Reports
Link Reports
Participant Reports
Query Reports
Manage Data Views
Manage Study Notifications
Manage Categories
Manage Thumbnail Images
Measure and Dimension Columns
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
Edit a List Design
Populate a List
Manage Lists
Export/Import a List Archive
R Reports
R Report Builder
Saved R Reports
R Reports: Access LabKey Data
Multi-Panel R Plots
Lattice Plots
Participant Charts in R
R Reports with knitr
Premium Resource: Show Plotly Graph in R Report
Input/Output Substitutions Reference
Tutorial: Query LabKey Server from RStudio
FAQs for LabKey R Reports
Premium RStudio Integration
Connect to RStudio
Set Up Docker with TLS
Connect to RStudio Workbench
Set Up RStudio Workbench
Edit R Reports in RStudio
Export Data to RStudio
Advanced Initialization of RStudio
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
Trace Query Dependencies
Query Web Part
LabKey SQL Examples
JOIN Queries
Calculated Columns
Premium Resource: Display Calculated Columns from Queries
Pivot Queries
Queries Across Folders
Parameterized SQL Queries
More LabKey SQL Examples
Linked Schemas and Tables
Controlling Data Scope
Ontology Integration
Load Ontologies
Concept Annotations
Ontology Column Filtering
Ontology Lookup
Ontology SQL
Data Quality Control
Quality Control Trend Reports
Define QC Trend Report
Use QC Trend Reports
QC Trend Report Guide Sets
Search
Search Administration
Integration with Spotfire
Premium Resource: Embed Spotfire Visualizations
Integration with AWS Glue
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
Premium Resource: Bulk Editing
Assay Data
Tutorial: Import Experimental / Assay Data
Step 1: Assay Tutorial Setup
Step 2: Infer an Assay Design from Spreadsheet Data
Step 3: Import Assay Data
Step 4: Visualize Assay Results
Step 5: Collect Experimental Metadata
Tutorial: Assay Data Validation
Assay Administrator Guide
Set Up Folder For Assays
Design a New Assay
Assay Design Properties
Design a Plate-Based Assay
Customize Plate Templates
Standard Plate-Based Assays
Specialty Plate-Based Assays
Participant/Visit Resolver Field
Manage an Assay Design
Export/Import Assay Design
Assay QC States: Admin Guide
Improve Data Entry Consistency & Accuracy
Assay Transform Script
Link Assay Data into a Study
Link-To-Study History
Assay Feature Matrix
Assay User Guide
Import Assay Runs
Multi-File Assay Runs
Work with Assay Runs
Assay QC States: User Guide
Exclude Assay Data
Re-import Assay Runs
Export Assay Data
Assay Terminology
ELISA Assay
Tutorial: ELISA Assay
ELISA Run Details View
ELISA Assay Reference
Enhanced ELISA Assay Support
ELISpot Assay
Tutorial: ELISpot Assay Tutorial
Import ELISpot Data
Review ELISpot Data
ELISpot Properties and Fields
Flow Cytometry
Flow Cytometry Overview
LabKey Flow Module
Set Up a Flow Folder
Tutorial: Explore 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
Import a Flow Workspace and Analysis
Edit Keywords
Add Sample Descriptions
Add Statistics to FCS Queries
Flow Module Schema
Analysis Archive Format
Add Flow Data to a Study
FCS keyword utility
FluoroSpot Assay
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: Link 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 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
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
Discovery Proteomics
Install Trans Proteomic Pipeline
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
Search and Process MS2 Data
Configure Common Parameters
Configure X!Tandem Parameters
Configure Mascot Parameters
Configure Sequest Parameters
Sequest Parameters
Configure Comet Parameters
Trigger MS2 Processing Automatically
Set Proteomics Search Tools Version
Explore the MS2 Dashboard
View an MS2 Run
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
MS2: File-based Module Resources
Work with Mascot Runs
Loading Public Protein Annotation Files
Using Custom Protein Annotations
Using ProteinProphet
Using Quantitation Tools
MaxQuant Module
Spectra Counts
Label-Free Quantitation
Combine X!Tandem Results
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 Assay Reference
Assay Request Tracker
Premium Resource: Using the Assay Request Tracker
Premium Resource: Assay Request Tracker Administration
Experiment Framework
Experiment Terminology
Experiment Runs
Run Groups
Experiment Lineage Graphs
Provenance Module: Run Builder
XAR Files
Import and Export a XAR File
Example 1: Review a Basic XAR.xml
Examples 2 & 3: Describe Protocols
Examples 4, 5 & 6: Describe LCMS Experiments
Life Science Identifiers (LSIDs)
LSID Substitution Templates
Record Lab Workflow
Tutorial: Lab Workflow Folder
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 Lab Workspace
Reagent Module
Samples
Create Sample Type
Sample Naming Patterns
Aliquot Naming Patterns
Add Samples
Premium Resource: Split Large Sample Upload
Manage Sample Types and Samples
Link Assay Data to Samples
Link Sample Data to Study
Sample Parents: Derivation and Lineage
Sample Types: Examples
Barcode Fields
Data Classes
Create Data Class
Studies
Tutorial: Longitudinal Studies
Step 1: Study Dashboards
Step 2: Study Reports
Step 3: Compare Participant Performance
Tutorial: Set Up a New Study
Step 1: Create Study Framework
Step 2: Import Datasets
Step 3: Identify Cohorts
Step 4: Integrate and Visualize Data
Install an Example Study
Study User Guide
Study Navigation
Cohorts
Participant Groups
Dataset QC States: User Guide
Study Administrator Guide
Study Management
Study Properties
Manage Datasets
Manage Visits or Timepoints
Study Schedule
Manage Locations
Manage Cohorts
Alternate Participant IDs
Alias Participant IDs
Manage Study 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
Study Demo Mode
Create a Study
Create and Populate Datasets
Import Data to a Dataset
Import From a Dataset Archive
Dataset Properties
Study: Reserved and Special Fields
Dataset System Fields
Tutorial: Inferring Datasets from Excel and TSV Files
Visits and Dates
Create Visits Manually
Edit Visits or Timepoints
Import Visit Map
Import Visit Names / Aliases
Continuous Studies
Study Visits and Timepoints FAQ
Export/Import/Reload a Study
Export a Study
Import a Study
Reload a Study
Study Object Files and Formats
Publish a Study
Publish a Study: Protected Health Information / PHI
Ancillary Studies
Refresh Data in Ancillary and Published Studies
Cohort Blinding
Shared Datasets and Timepoints
How is Study Data Stored in LabKey Server?
Create a Vaccine Study Design
Vaccine Study: Data Storage
Premium Resource: LabKey Data Finder
Electronic Health Records (EHR)
Premium Resource: EHR: Animal History
Premium Resource: EHR: Animal Search
Premium Resource: EHR: Data Entry
Premium Resource: EHR: Data Entry Development
Premium Resource: EHR: Lookups
Premium Resource: EHR: Genetics Algorithms
Premium Resource: EHR: Administration
Premium Resource: EHR: Connect to Sample Manager
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
Premium Resource: EHR: Compliance and Training Folder
Premium Resource: EHR: Trigger Scripts
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 Development
Extending SND Tables
XML Import of Packages
Enterprise Master Patient Index Integration
Specimen Tracking (Legacy)
Panorama: Targeted Mass Spectrometry
Configure Panorama Folder
Panorama Data Import
Panorama Experimental Data Folder
Panorama: Skyline Document Management
Panorama: Skyline Replicates View
Panorama: Protein/Molecule List Details
Panorama: Skyline Lists
Panorama: Skyline Annotation Data
Panorama: Skyline Audit Log
Panorama: Calibration Curves
Panorama: Figures of Merit and Pharmacokinetics (PK)
Panorama: Instruments Summary and QC Links
Working with Small Molecule Targets
Panorama: Heat Maps
Panorama Multi-Attribute Method Folder
Panorama MAM Reports
Panorama: Crosslinked Peptides
Panorama Chromatogram Library Folder
Using Chromatogram Libraries
Panorama: Reproducibility Report
Panorama QC Folders
Panorama QC Dashboard
Panorama: Instrument Utilization Calendar
Panorama QC Plots
Panorama QC Plot Types
Panorama QC Annotations
Panorama: Pareto Plots
Panorama: iRT Metrics
Panorama: Configure QC Metrics
Panorama: Outlier Notifications
Panorama QC Guide Sets
Panorama: Chromatograms
Panorama and Sample Management
Collaboration
Files
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
Using the Files Repository
View and Share Files
Controlling File Display via the URL
Import Data from Files
Linking Assays with Images and Other Files
Linking Data Records to Image Files
File Metadata
File Administrator Guide
Files Web Part Administration
File Root Options
Troubleshoot Pipeline and Files
File Terminology
Transfer Files with WebDAV
File Transfer Module / Globus File Sharing
S3 Cloud Data Storage
AWS Identity Credentials
Configure Cloud Storage
Use Files from Cloud Storage
Cloud Storage for File Watchers
Messages
Use Message Boards
Configure Message Boards
Object-Level Discussions
Wikis
Create a Wiki
Wiki Admin Guide
Manage Wiki Pages
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: Web Parts Embedded in Wiki Pages
Web Part Configuration Properties
Add Screenshots to a Wiki
Issue/Bug Tracking
Tutorial: Issue 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
CDISC ODM XML Integration
Workflow Module
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
Contact Information
How to Cite LabKey Server
Development
Set Up a Development Machine
Gradle Build Overview
Build LabKey from Source
Build from Source (or Not)
Customize the Build
Node.js Build Dependency
Git Ignore Configurations
Build Offline
Gradle Cleaning
Gradle Properties
Gradle: How to Add Modules
Gradle: Declare Dependencies
Gradle Tips and Tricks
Premium Resource: Artifactory Set Up
Premium Resource: NPMRC Authentication File
Create Production Builds
Set up OSX for LabKey Development
Troubleshoot Development Machines
Premium Resource: IntelliJ Reference
Run in Development Mode
LabKey Client APIs
API Resources
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
Premium Resource: JavaScript Security API Examples
JavaScript Reports
Export Data Grid as a Script
Premium Resource: Custom Participant View
Example: Master-Detail Pages
Custom Button Bars
Premium Resource: Invoke JavaScript from Custom Buttons
Premium Resource: Custom Buttons for Large Grids
Premium Resource: Type-Ahead Entry Forms
Premium Resource: Sample Status Demo
Insert into Audit Table via API
Programming the File Repository
Vocabulary Domains
Declare Dependencies
Using ExtJS with LabKey
Naming & Documenting JavaScript APIs
How to Generate JSDoc
JsDoc Annotation Guidelines
Naming Conventions for JavaScript APIs
Java API
LabKey JDBC Driver
Security Bulk Update via API
Perl API
Python API
Premium Resource: Python API Demo
Premium Resource: Download a File with Python
Rlabkey Package
Troubleshoot Rlabkey
Premium Resource: Example Code for QC Reporting
SAS Client API Library
SAS Setup
SAS Macros
SAS Demos
HTTP Interface
Examples: Controller Actions / API Test Page
Example: Access APIs from Perl
External Tool Access
API Keys
External ODBC and JDBC Connections
ODBC: Configure Windows Access
ODBC: Configure OSX/Mac Access
ODBC: External Tool Connections
ODBC: Using SQL Server Reporting Service (SSRS)
Compliant Access via Session Key
Develop Modules
Tutorial: Hello World Module
Map of Module Files
Module Loading Using the Server UI
Module Editing Using the Server UI
Example Modules
Tutorial: File Based Module Resources
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
Transform Scripts
Example Workflow: Develop a Transformation Script
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: SQL Script Conventions
Modules: Domain Templates
Java Modules
Module Architecture
Tutorial: Hello World Java Module
LabKey Containers
Implementing Actions and Views
Implementing API Actions
Integrating with the Pipeline Module
Integrating with the Experiment API
Using SQL in Java Modules
Database Development Guide
HotSwapping Java classes
Modules: Custom Login Page
Modules: Custom Site Welcome Page
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: User Interface
ETL: Create a New ETL
ETL: Planning
ETL: Attributes
ETL: Target Options
ETL: Column Mapping
ETL: Transform Types and Tasks
ETL: Manage Remote Connections
ETL: Filter Strategies
ETL: Schedules
ETL: Transactions
ETL: Queuing ETL Processes
ETL: Stored Procedures
ETL: Stored Procedures in MS SQL Server
ETL: Stored Procedures in PostgreSQL
ETL: Check For Work From a Stored Procedure
ETL: Logs and Error Handling
ETL: Examples
ETL: Module Structure
Premium Resource: ETL Best Practices
Deploy Modules to a Production Server
Main Credits Page
Module Properties
module.properties Reference
Common Development Tasks
Premium Resource: Content Security Policy Development Best Practices
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
Cross-Site Request Forgery (CSRF) Protection
Premium Resource: Fetching CSRF Token
Premium Resource: Changes in JSONObject Behavior
Profiler Settings
Using loginApi.api
Use IntelliJ for XML File Editing
Premium Resource: Manual Index Creation
Premium Resource: LabKey Coding Standards and Practices
Premium Resource: Best Practices for Writing Automated Tests
Premium Resource: Server Encoding
Premium Resource: ReactJS Development Resources
Premium Resource: Feature Branch Workflow
Premium Resource: Develop with Git
Premium Resource: Git Branch Naming
Premium Resource: Issue Pull Request
LabKey Open Source Project
Release Schedule
Previous Releases
Previous Release Details
Branch Policy
Testing and Code Quality Workflow
Run Automated Tests
Tracking LabKey Issues
Security Issue Evaluation Policy
Submit Contributions
CSS Design Guidelines
Documentation Style Guide
Check In to the Source Project
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
Project and Folder Settings
Create a Project or Folder
Manage Projects and Folders
Enable a Module in a Folder
Export / Import a Folder
Export and Import Permission Settings
Manage Email Notifications
Establish Terms of Use
Workbooks
Shared Project
Build User Interface
Premium Resource: Custom Home Page Examples
Page Admin Mode
Add Web Parts
Manage Web Parts
Web Part Inventory
Use Tabs
Add Custom Menus
Web Parts: Permissions Required to View
Security
Best Practices for System Security
Configure Permissions
Security Groups
Global Groups
Site Groups
Project Groups
Guests / Anonymous Users
Security Roles Reference
Role/Permissions Matrix
Administrator Permissions Matrix
Matrix of Report, Chart, and Grid Permissions
Privileged Roles
Developer Roles
Storage Roles
Premium Resource: Add a Custom Security Role
User Accounts
My Account
Add Users
Manage Users
Manage Project Users
Premium Resource: Limit Active Users
Authentication
Configure Database Authentication
Passwords
Password Reset
Configure LDAP Authentication
Configure SAML Authentication
Configure CAS Authentication
Configure CAS Identity Provider
Configure Duo Two-Factor Authentication
Configure TOTP Two-Factor Authentication
Create a netrc file
Virus Checking
Test Security Settings by Impersonation
Premium Resource: Best Practices for Security Scanning
Compliance
Compliance: Overview
Compliance: Checklist
Compliance: Settings
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
Project Locking and Review Workflow
Admin Console
Site Settings
Usage/Exception Reporting
Look and Feel Settings
Page Elements
Web Site Theme
Email Template Customization
Experimental Features
Manage Missing Value Indicators / Out of Range Values
Short URLs
Configure System Maintenance
Configure Scripting Engines
Configure Docker Host
External Redirect Hosts
LDAP User/Group Synchronization
Proxy Servlets
Premium Resource: Plotly Dash Demo
Audit Log / Audit Site Activity
SQL Query Logging
Site HTTP Access Logs
Audit Log Maintenance
Export Diagnostic Information
Actions Diagnostics
Cache Statistics
Loggers
Memory Usage
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: File Name Patterns
File Watcher Examples
Premium Resource: Run Pipelines in Parallel
Enterprise Pipeline with ActiveMQ
ActiveMQ JMS Queue
Configure the Pipeline with ActiveMQ
Configure Remote Pipeline Server
Troubleshoot the Enterprise Pipeline
Install LabKey
Supported Technologies
Install on Linux
Install on Windows
Set Application Properties
Common Install Tasks
Service File Customizations
Use HTTPS with LabKey
SMTP Configuration
Install and Set Up R
Configure an R Docker Engine
Determine Available Graphing Functions
Control Startup Behavior
Server Startup Properties
ExtraWebapp Resources
Sending Email from Non-LabKey Domains
Deploying an AWS Web Application Firewall
Install Microsoft SQL Server
GROUP_CONCAT Install
PremiumStats Install
Troubleshoot Installation and Configuration
Installation Error Messages
Collect Debugging Information
Example Hardware/Software Configurations
Premium Resource: Reference Architecture / System Requirements
Community Edition Modules
Additional Source Modules
Upgrade LabKey
Upgrade on Linux
Upgrade on Windows
Migrate Configuration to Application Properties
Premium Resource: Upgrade JDK on AWS Ubuntu Servers
LabKey Releases and Upgrade Support Policy
External Schemas and Data Sources
External PostgreSQL Data Sources
External Microsoft SQL Server Data Sources
External MySQL Data Sources
External Oracle Data Sources
External SAS/SHARE Data Sources
External Redshift Data Sources
Backup and Maintenance
Backup Guidelines
An Example Backup Plan
Example Scripts for Backup Scenarios
Restore from Backup
Premium Resource: Change the Encryption Key
Use a Staging Server
Troubleshoot LabKey Server
Sample Manager
Use Sample Manager with LabKey Server
Use Sample Manager with Studies
LabKey ELN
Notebook Dashboard
Author a Notebook
Notebook References
Notebook ID Generation
Manage Tags
Notebook Review
Notebook Amendments
Notebook Templates
Export Notebook
Configure Puppeteer
ELN: Frequently Asked Questions
Biologics LIMS
Biologics: Navigate
Introduction to LabKey Biologics
Release Notes: Biologics
Biologics Tutorials
Biologics Basics: Navigate and Search
Biologics Tutorial: Add Sequences to the Registry
Biologics Tutorial: Register Samples
Biologics Tutorial: Work with Mixtures and Batches
Biologics Tutorial: Create a New Biologics Project
Customizing Biologics: Purification Systems
Biologics: Search Options
Biologics: Projects and Folders
Biologics: Bioregistry
Create Registry Sources
Register Nucleotide Sequences
Register Protein Sequences
Register Leaders, Linkers, and Tags
Vectors, Constructs, Cell Lines, and Expression Systems
Edit Registry Sources
Registry Reclassification
Biologics: Terminology
Protein Sequence Annotations
CoreAb Sequence Classification
Biologics: Chain and Structure Formats
Molecules, Sets, and Molecular Species
Register Molecules
Molecular Physical Property Calculator
Compounds and SMILES Lookups
Entity Lineage
Customize the Bioregistry
Bulk Registration of Entities
Use the Registry API
Biologics: Samples
Biologics: Create Samples
Biologics: Manage Samples
Print Labels with BarTender
Biologics: Assay Data
Biologics: Upload Assay Data
Biologics: Work with Assay Data
Biologics: Media Registration
Managing Ingredients and Raw Materials
Registering Mixtures (Recipes)
Registering Batches
Biologics: Workflow
Biologics: Create Workflow Job
Biologics: Storage Management
Shared Storage
Biologics Administration
Biologics: Grids, Detail Pages, and Entry Forms
Biologics: Protect Sequence Fields
Biologics: Users, Groups, and Roles
Biologics Admin: Charts
Biologics Admin: Set Up Assays
Biologics Admin: Assay Integration
Biologics Admin: URL Properties
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LabKey Support Portals
Premium Resource: Training Materials
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FAQ: Frequently Asked Questions
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DataSpace: Learn About
DataSpace: Find Subjects
DataSpace: Plot Data
DataSpace: View Data Grid
DataSpace: Monoclonal Antibodies
Documentation Archive
Release Notes: 23.11 (November 2023)
What's New in 23.11
Release Notes: 23.7 (July 2023)
What's New in 23.7
Release Notes: 23.3 (March 2023)
What's New in 23.3
Release Notes: 22.11 (November 2022)
What's New in 22.11
Release Notes 22.7 (July 2022)
What's New in 22.7
Release Notes 22.3 (March 2022)
What's New in 22.3
Release Notes 21.11 (November 2021)
What's New in 21.11
Release Notes 21.7 (July 2021)
What's New in 21.7
Release Notes 21.3 (March 2021)
What's New in 21.3
Release Notes 20.11 (November 2020)
What's New in 20.11
Release Notes 20.7
What's New in 20.7
Release Notes 20.3
What's New in 20.3
Release Notes 19.3
What's New in 19.3
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
Release Notes 18.2
What's New in 18.2
Release Notes 18.1
What's New in 18.1
Release Notes 17.3
Release Notes 17.2
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