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Documentation: Version 16.1

Introduction

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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

Data Basics - Build applications from user interface panels and views on underlying data.
Laboratory Data - Work with instrument-derived data.
Research Studies - Integrate heterogeneous data in longitudinal/cohort studies.
Collaboration - Set up file repositories, message boards, and issue trackers.
Development - Developer resources.
Administration - Create new projects, configure security, advanced installation.
Products and Services - LabKey Server products and services.

Documentation Highlights

What's New in 16.1 - Highlighted features in the 16.1 release.
Release Notes 16.1 - Detailed feature list.
Upcoming Features in 16.2 - Features in development for the 16.2 release.

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Current Folder & Subfolders

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Assays

Files and Attachments

Issues

Lists

Messages

Ontology Concepts

Projects and Folders

Study Datasets

Study Subjects

Wiki Pages

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10 Minute Tutorial

Install LabKey Server (Quick Install)

What's New in 16.1

Release Notes 16.1

Upcoming Features in 16.2

Platform Overview

FAQ - Frequently Asked Questions

Showcase of Installations

How to Cite LabKey Server

LabKey Terminology/Glossary

Archive: Documentation

What's New in 15.3

Release Notes 15.3

What's New in 15.2?

Release Notes 15.2

What's New in 15.1?

	Release Notes 15.1
	LabKey Argos

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

Build User Interface

	Add Web Parts
	Manage Web Parts
	Web Part Inventory
	Use Tabs
	Add Custom Menus
	Web Parts: Permissions Required to View

Data Grids: Basics

Customize Views

Saved Filters and Sorts

Join Columns from Multiple Tables

Participant Views

Query Scope: Filter by Folder

Field Properties Reference

URL Field Property

Conditional Formats

Date & Number Display Formats

Date and Number Formats Reference

Reports and Visualizations

Display a Report or View

Data Views Browser

Manage Reports and Views

Manage Categories

Manage Thumbnail Images

Attachment Reports

Participant 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

Why Is a Column Not Available for Charting?

	Advanced Views / External Reports
	Chart Views
	Crosstab Views

	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
	Parameterized SQL Queries
	SQL Examples: JOIN, Calculated Columns, GROUP BY
	Cross-Folder Queries
	SQL Synonyms

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

Preparing Data for Import

	List Tutorial: Set Up
	Create a Joined View to Investigate Results
	Add a URL Property

Create and Populate Lists

	Create a List by Defining Fields
	Populate a List
	Import a List Archive

Edit a List Design

Choose a Primary Key

Search Administration

Natural Language Processing Pipeline (NLP)

	Configure Natural Language Processing
	Process Files Using Natural Language Processing

Laboratory Data

Tutorial: Design a General Purpose Assay (GPAT)

	Assay Tutorial Set Up
	Infer an Assay Design from Spreadsheet Data
	Import Assay Data
	Work with Assay Data
	Data Validation
	Integrate Assay Data into a Study

ELISA Assay Tutorial

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

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

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 Well Details

Finalize a Dataset View and Export

Tutorial: Perform a LabKey Flow 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

Tutorial: Import Flow Data from FCS Express

Reagent Inventory

FCS keyword utility

Flow Team Members

	Microarray Assay Tutorial
	Expression Matrix Assay Tutorial
	Microarray Properties

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

Working with Small Molecule Targets

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

View, Filter and Export Mascot Runs

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

Label-Free Quantitation

Combine XTandem Results

Panorama - Targeted Proteomics

	Configure Panorama Folder
	Panorama QC Dashboard
	Panorama Quality Control
	Panorama Document Revision Tracking

Proteomics Team

Genomics Workflows

	Set Up a Genotyping Dashboard
	Example Workflow: LabKey and Galaxy
	Example Workflow: LabKey and Illumina
	Example Workflow: LabKey and PacBio
	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

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)

Research Studies

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 and Populate Datasets

Create a Dataset from a File

Create a Dataset by Defining Fields

Create Multiple Dataset Definitions from a TSV File

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

Custom Study Properties

Manage Datasets

Manage Visits or Timepoints

Manage Locations

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

Continuous Studies

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

Specimen Tracking

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

Laboratory Information Management System (LIMS)

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)

Share and View Files

File Sharing and URLs

Import Data from Files

File Administrator Guide

Files Web Part Administration

Upload Files: WebDAV

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
	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

	Use Message Boards
	Administer Message Boards

Wiki Admin Guide

Copy Wiki Pages

Wiki User Guide

Wiki Syntax: Macros

Special Wiki Pages

Embed Live Content in Wiki Pages or Messages

	Examples: Embedded Web Parts
	Web Part Configuration Properties

Add Screenshots to a Wiki

Manage Wiki Attachment List

Wiki: Discussion Link

Issue/Bug Tracking

	Using the Issue Tracker
	Administering the Issue Tracker

Electronic Data Capture (EDC)

	Survey Designer: Basics
	Survey Designer: Customization
	Survey Designer: Reference
	Survey Designer: Example Questions
	Survey Designer Examples
	REDCap Survey Data Integration

Adjudication Module

	Set Up an Adjudication Folder
	Initiate an Adjudication Case
	Make an Adjudication Determination
	Monitor Adjudication
	Role Guide: Adjudicator
	Role Guide: Adjudication Lab Personnel

LabKey Client APIs

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

Adding Views to a Data Grid with JavaScript

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

	Prototype LabKey JDBC Driver
	Remote Login API
	Security Bulk Update via API

Rlabkey Package

Troubleshooting Rlabkey Connections

	SAS Setup
	SAS Macros
	SAS Security
	SAS Demos

	Examples: Controller Actions
	Example: Access APIs from Perl

Develop Modules

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-Based Queries: Metadata

Module R Reports

Module-Based Reports: Metadata

Module HTML and Web Parts

Providing a Custom Footer

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
	Warnings in Tranformation Scripts

Tutorial: Extract-Transform-Load (ETL)

	ETL Tutorial: Set Up
	ETL Tutorial: Run an ETL
	ETL Tutorial: Create a New ETL

ETL: User Interface

ETL: Schedules and Options

ETL: Column Mapping

ETL: Queue an ETL From Another ETL

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

	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

Main Credits Page

Module Properties Reference

Common Development Tasks

Trigger Scripts

Availability of Server-side Trigger Scripts

Script Pipeline: Running R and Other Scripts in Sequence

How To Find schemaName, queryName & viewName

LabKey/Rserve Setup Guide

Context Paths: contextPath, containerPath, webpartContext

Web Application Security

	HTML Encoding
	Cross-Site Request Forgery (CSRF) Protection

LabKey Open Source Project

Release Schedule

LabKey Scrum FAQ

Developer Email List

Test Procedures

Running Automated Tests

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

Creating Production Builds

Enlisting in the Version Control Project

Enlisting Proteomics Binaries

Customizing the Build

Machine Security

Notes on Setting up a Mac for LabKey Development

Developer Reference

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

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

Community Modules

Establish Terms of Use

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 Table

	My Account
	Manage Project Users

Configure Database Authentication

	Passwords
	Password Reset & Security

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

Usage/Exception Reporting - Details

Look and Feel Settings

	Branding
	Web Site Theme

Email Customization

Experimental Features

Manage Missing Value Indicators / Out of Range Values

Configure System Maintenance

Configure Scripting Engines

Audit Site Activity

SQL Query Logging

Actions Diagnostics

Cache Statistics

Running Threads

Query Performance

Site/Container Validation

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 and Thread 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

	Manual Upgrade Checklist
	Manual Upgrade Script for MacOSX, Solaris and Unsupported Linux Distributions
	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

Products and Services

LabKey Server Editions

	Training
	Custom Community Modules

LabKey Biologics

Panorama Partners Program

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