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Install Prerequisites for the Enterprise Pipeline

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Install Prerequisites for the Enterprise Pipeline

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In order to install the LabKey Enterprise Pipeline, you will first need to install and configure the following prerequisite software:

Installation of LabKey Server
JMS Queue (ActiveMQ)
Conversion Service (convert MS2 output to mzXML). Optional. Only required if you plan to convert files to mzXML format in your pipeline

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Documentation Home

Getting Started with LabKey Server

Data Grid Tutorial

System Integration: Instruments and Software

LabKey Server Solutions

	Academic Research Solutions
	Pharma & Biotech Solutions
	Clinical & Provider Solutions

Install LabKey Server (Quick Install)

What's New in 17.1

Release Notes 17.1

Upcoming Features in 17.2

Demos and Videos

FAQ - Frequently Asked Questions

How to Cite LabKey Server

LabKey Terminology/Glossary

Archive: Documentation

What's New in 16.3

Release Notes 16.3

What's New in 16.2

Release Notes 16.2

What's New in 16.1

Release Notes 16.1

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

What's New 17.2

Release Notes 17.2

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

Filtering Expressions

Column Summary Statistics

Customize Grid Views

Saved Filters and Sorts

Join Columns from Multiple Tables

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 Visualizations

Report Web Part: Display a Report or Chart

Data Views Browser

Column Visualizations

	RStudio and LabKey Server
	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
	R Tutorial Video

JavaScript Reports

Attachment Reports

Participant Reports

Manage Reports and Charts

Manage Categories

Manage Thumbnail Images

Measure and Dimension Columns

	Advanced Reports / External Reports
	Chart Views
	Crosstab Reports

LabKey SQL Tutorial

SQL Query Browser

LabKey SQL Reference

Lookups: SQL Syntax

Create a SQL Query

Edit SQL Query Source

Query Metadata: Examples

Edit Query Properties

Query Web Part: 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

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

Data Quality Control

	List Tutorial: Setup
	Create a Joined Grid
	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

Laboratory 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

ELISA Assay Tutorial

ELISpot Assay Tutorial

	Import ELISpot Data
	Review ELISpot Data

ELISpot Properties

LabKey Flow Module

Supported FlowJo Versions

Flow Cytometry Overview

Tutorial: Import a Flow Workspace

Step 1: Set Up a Flow Folder

Step 2: Upload Files to Server

Step 3: Import a Flow Workspace and Analysis

FCS File Resolution

Step 4: Customize Your Grid View

Step 5: Examine Graphs

Step 6: Examine Well Details

Step 7: Export Flow Data

Tutorial: Perform a LabKey Flow Analysis

	Step 1: Define a Compensation Calculation
	Step 2: Define an Analysis
	Step 3: Apply a Script
	Step 4: 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

FCS keyword utility

Flow Team Members

FluoroSpot Assay

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

HPLC - High-Performance Liquid Chromatography

Luminex Assay Tutorial Level I

	Setup Luminex Tutorial Project
	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 7: Use Guide Sets for QC
	Step 8: 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 Assay Tutorial
	Expression Matrix Assay Tutorial
	Microarray Properties

NAb (Neutralizing Antibody) Assays

NAb Assay Tutorial

	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

Work with Multiple Viruses per Plate

NAb Plate File Formats

Customize NAb Plate Template

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
	Proteomics Video

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

Compare MS2 Runs

Compare ProteinProphet

Export MS2 Runs

Working with Small Molecule Targets

Export Spectra Libraries

View, Filter and Export All MS2 Runs

Work with Mascot Runs

Loading Public Protein Annotation Files

Using Custom Protein Annotations

Using ProteinProphet

Using Quantitation Tools

Protein Expression Matrix Assay

Link Protein Expression Data with Annotations

Label-Free Quantitation

Combine XTandem Results

Panorama - Targeted Proteomics

	Configure Panorama Folder
	Panorama QC Dashboard
	Panorama QC Plots
	Panorama Plot Types
	Panorama QC Annotations
	Panorama QC Guide Sets
	Pareto Plots
	Panorama: Clustergrammer Heat Maps
	Panorama Document Revision Tracking

Proteomics Team

Signal Data Assay

Assay Administrator Guide

Assay Feature Matrix

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

Copy Assay Data into a Study

Copy-To-Study History

Experiment Descriptions & Archives (XARs)

Experiment Terminology

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
	Reimport Assay Runs

	Import Sample Sets
	Samples: Unique IDs
	View SampleSets and Samples
	Link Assay Data to Sample Sets
	Parent Samples: Derivation and Lineage
	Sample Sets: Examples
	'Active' Sample Set

Electronic Laboratory Notebooks (ELN)

Tutorial: Electronic Lab Notebook

	Step 1: Create the User Interface
	Step 2: Import Lab Data
	Step 3: Link Assays to Samples
	Step 4: Using and Extending the ELN

Assay Request Tracker

	Assay Request Tracker: User Documentation
	Assay Request Tracker: Administrator Documentation

Reagent Inventory

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: Visualizations and Reports

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 via Copy/Paste

Import From a Dataset Archive

Create Pipeline Configuration File

Import Study Data From REDCap Projects

Dataset Properties

Edit Dataset Properties

Dataset System Fields

Use Visits or Timepoints/Dates

	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

Study Data Model

Linking Data Records with External Files

Specimen Tracking

Specimen Request Tutorial

	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

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)

Electronic Health Records (EHR)

	EHR: Animal History
	EHR: Animal Search
	EHR: Data Entry
	EHR: Administration
	EHR Team

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

Using the Files Repository

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
	Pipeline Protocols

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
	Object-Level Discussions

Wiki Admin Guide

Copy Wiki Pages

Wiki User Guide

Wiki Syntax: Macros

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
	Administering the Issue Tracker

Workflow Module

Workflow Tutorial

	Step 1: Set Up Workflow Tutorial
	Step 2: Run Sample Workflow Process
	Step 3: Workflow Process Definition
	Step 4: Customize Workflow Process Definition

Workflow Process Definition

Electronic Data Capture (EDC)

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

Adjudication Module

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

Tours for New Users

LabKey Client APIs

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 Video: Building Reports and Custom User Interfaces

JavaScript API - Samples

Adding Report to a Data Grid with JavaScript

Export Data Grid as a Script

Export Chart as JavaScript

Custom HTML/JavaScript Participant Details View

Custom Button Bars

Insert into Audit Table via API

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

	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

Compliant Access via Session Key

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

Creating Production Builds

Encoding in Tomcat 7

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 R Reports
	Module HTML and Web Parts

Modules: JavaScript Libraries

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 Process
	ETL Tutorial: Create a New ETL Process

ETL: User Interface

ETL: Configuration and Schedules

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

	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: Query Metadata

Modules: Report Metadata

Modules: Custom Footer

Modules: SQL Scripts

Modules: Database Transition Scripts

Modules: Domain Templates

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 R and Other Scripts in Sequence

How To Find schemaName, queryName & viewName

LabKey/Rserve Setup Guide

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

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
	Site Groups
	Project Groups
	Guests / Anonymous Users

Security Roles Reference

	Site Administrator
	Matrix of Report, Chart, and Grid Permissions
	Role / Permissions Table

	My Account
	Manage Project Users

Configure Database Authentication

	Passwords
	Password Reset & Security

Configure SAML Authentication

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

	Compliance: Protected Health Information
	Compliance Settings
	Compliance Terms of Use
	Compliance Module Logging

Usage/Exception Reporting - Details

Look and Feel Settings

	Branding
	Web Site Theme

Email Template 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
	Third-Party Components and Licenses

Install a Remote Pipeline Server via the Windows Installer

PremiumStats Install

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

	Example Hardware/Software Configuration
	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 Linux, MacOSX, and Solaris
	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 Natural Language Pipeline (NLP)

	Configure LabKey NLP
	Process Files Using Natural Language Pipeline (NLP)
	Document Abstraction Workflow
	Automatic Assignment for Abstraction
	Manual Assignment for Abstraction
	Document Abstraction
	Review Document Abstraction

LabKey Biologics

LabKey Biologics: Preview

Panorama Partners Program

LabKey User Conference Resources

	LabKey User Conference 2016
	LabKey User Conference 2015
	LabKey User Conference 2014
	LabKey User Conference 2013
	LabKey User Conference 2012
	LabKey User Conference 2011

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