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LabKey Biologics
Biologics: Workflow Management
Documentation: Version 20.7
Biologics: Workflow Management
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The following topics explain how to assign and track laboratory tasks, such as creating new batches of media and running assays on samples:
Biologics Workflow
Biologics Admin: Service Request Tracker Set Up
Related Topics
Premium Resource: Assay Request Tracker Administration
- Explains how to customize the system, such as populating the dropdowns with custom values.
Issue Tracker: Administration
- Explains how to administer the issue tracking system generally, such as controlling the "Assigned To" dropdown, adding custom fields, etc.
Video Resources
Video: Quick Look: Managing Assay Requests in LabKey Biologics
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Step 1: Customize Your Grid View
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Step 5: Flow Quality Control
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Tutorial: Perform a LabKey Flow Analysis
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Step 1: Define a Compensation Calculation
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Step 3: Apply a Script
Step 4: View Results
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Edit Keywords
Add Sample Descriptions
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Add Statistics to FCS Queries
Flow Module Schema
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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
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Expression Matrix Assay Tutorial
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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
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Search and Process MS2 Data
Configure Common Parameters
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Configure Mascot Parameters
Configure Sequest Parameters
Sequest Parameters
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Trigger MS2 Processing Automatically
Set Proteomics Search Tools Version
Explore the MS2 Dashboard
View an MS2 Run
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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
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
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Customize NAb Plate Template
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Signal Data Assay
Assay Administrator Guide
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Set Up Folder For Assays
Assay Designs and Types
Design a New Assay
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Design a Plate-Based Assay
Customize Plate Templates
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Participant/Visit Resolver Field
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Assay QC States - Admin Guide
Improve Data Entry Consistency & Accuracy
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Multi-File Assay Runs
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Export Assay Data
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Premium Resource: Using the Assay Request Tracker
Premium Resource: Assay Request Tracker Administration
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XAR Terminology
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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 LCMS2 Experiments
Life Science Identifiers (LSIDs)
LSID Substitution Templates
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 Module
Data Classes
Create Data Class
Sample Types
Create Sample Type
Samples: Generate Unique IDs
Import Samples
View Sample Types and Samples
Link Assay Data to Samples
Parent Samples: Derivation and Lineage
Sample Types: Examples
Provenance Module: Run Builder
Longitudinal 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
Step 5: Add Specimen Data
Install an Example Study
Study User Guide
Study Navigation
Cohorts
Participant Groups
Comments
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 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
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
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
Ancillary Studies
Shared Datasets and Timepoints
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 Data Tables
Import FreezerPro Data
Delete Specimens
Specimen Fields 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
Using Samples 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: Data Entry Development
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
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
Extending SND Tables
XML Import of Packages
Enterprise Master Patient Index Integration
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 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 Data Pipeline and File Repository
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
Use the Enterprise Pipeline
Troubleshoot the Enterprise Pipeline
Messages
Use Message Boards
Configure Message Boards
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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
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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
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
Tours for New Users (Deprecated)
Hopscotch Options for Tours (Deprecated)
Contact Information
How to Cite LabKey Server
Development
Set Up a Development Machine
Access the Source Code
Add the Proteomics Binaries
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Build LabKey from Source
Building from Source (or Not)
Customize the Build
Node.js Build Dependency
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Build Offline
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Gradle: How to Add Modules
Gradle: Declare Dependencies
Gradle Tips and Tricks
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Premium Resource: NPMRC Authentication File
Create Production Builds
Machine Security
Notes on Setting up OSX for LabKey Development
Troubleshoot Development Machines
Premium Resource: IntelliJ Reference
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
Adding a Report to a Data Grid with JavaScript
Export Data Grid as a Script
Custom HTML/JavaScript Participant Details View
Premium Resource: Enhanced Custom Participant 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
Using ExtJS with LabKey
Search API Documentation
Naming & Documenting JavaScript APIs
How to Generate JSDoc
JsDoc Annotation Guidelines
Naming Conventions for JavaScript APIs
Java API
LabKey JDBC Driver
Deprecated: 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
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SAS Macros
SAS Security
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Examples: Controller Actions / API Test Page
Example: Access APIs from Perl
ODBC Connections
ODBC: Configure Windows Access
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ODBC: Using SQL Server Reporting Service (SSRS)
API Keys
Compliant Access via Session Key
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Tutorial: Hello World Module
Map of Module Files
Module Loading Using the Server UI
Module Editing Using the Server UI
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: SQL Script Conventions
Modules: Domain Templates
Modules: Java
Module Architecture
Tutorial: Hello World Java Module
Getting Started with the Demo 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
GWT Integration
GWT Remote Services
Database Development Guide
Java Testing Tips
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: Create a New ETL
ETL: Planning
ETL: Filter Strategies and Target Options
ETL: Schedules
ETL: Column Mapping
ETL: Transactions
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: User Interface
ETL: Examples
ETL: Reference
Premium Resource: ETL Best Practices
Deploy Modules to a Production Server
Premium Resource: Migrate Module from SVN to GitHub
Upgrade Modules
Main Credits Page
module.properties Reference
module.xml Reference
Common Development Tasks
Premium Resource: Manual Index Creation
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
Premium Resource: Fetching CSRF Token
Profiler Settings
Using loginApi.api
Configuring IntelliJ for XML File Editing
Premium Resource: LabKey Coding Standards and Practices
Premium Resource: Best Practices for Writing Automated Tests
Premium Resource: ReactJS Development Resources
Premium Resource: Feature Branch Workflow
Premium Resource: Develop with Git
Premium Resource: Git Branch Naming
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LabKey Open Source Project
Release Schedule
Previous Releases
Previous Release Details
Open Source Project: Entering Issues
Branch Policy
Test Procedures
Run Automated Tests
Hotfix Policy
Security Issue Evaluation Policy
Submit Contributions
CSS Design Guidelines
UI Design Patterns
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
Page Admin Mode
Add Web Parts
Manage Web Parts
Web Part Inventory
Use Tabs
Add Custom Menus
Web Parts: Permissions Required to View
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
Configure LDAP Authentication
Configure SAML Authentication
Configure CAS Single Sign On Authentication (SSO)
Configure CAS Identity Provider
LDAP User/Group Synchronization
Configure Duo 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: 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
Look and Feel Settings
Page Elements
Web Site Theme
Email Template Customization
Experimental Features
External Redirect Hosts
Manage Missing Value Indicators / Out of Range Values
Short URLs
Configure System Maintenance
Configure Scripting Engines
Proxy Servlets
Audit Site Activity
SQL Query Logging
Export Diagnostic Information
Actions Diagnostics
Cache Statistics
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: File Name Patterns
File Watcher Examples
Install LabKey
Supported Technologies
Example Hardware/Software Configurations
Premium Resource: Reference Architecture / System Requirements
Installation Checklists
Install on Linux: Main Components
Install on Windows: Main Components
Installation: Tomcat Configuration
Installation: SMTP, Encryption, LDAP, and File Roots
Installation: Third-Party Components
Troubleshoot Server Installation and Configuration
Installation Error Messages
Collect Debugging Information
Common Install Tasks
Configure Tomcat Webapp Memory
Creating & Installing SSL/TLS Certificates on Tomcat
Install Microsoft SQL Server
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
Server Bootstrap Properties
Set Up Robots.txt and Sitemaps
GROUP_CONCAT Install
Sending Email from Non-LabKey Domains
PremiumStats Install
Deploying an AWS Web Application Firewall
Configure the Virtual Frame Buffer on Linux
Community Edition Modules - Descriptions
Additional Source Modules
Upgrade LabKey
Manual Upgrade Checklist for Linux and OSX
Upgrade Script for Linux and OSX
Windows Upgrade
Premium Resource: Upgrade OpenJDK on AWS Ubuntu Servers
LabKey Releases and Upgrade Support Policy
Backup and Maintenance
Backup Checklist
An Example Backup Plan
Example Scripts for Backup Scenarios
Post a Site Down Message
Tips for Configuring a Staging Server
Example of a Large-Scale Installation
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
Customizing Biologics: Purification Systems
Biologics: Terminology
Biologics: 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
Biologics: Import Samples
Biologics: Manage Samples
Samples Within LabKey Server
Sample Comparison Report
Biologics: Assay Management
Biologics: Upload Assay Data
Biologics Assay Data
Biologics: 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 Pages, and Entry Forms
Biologics Admin: Charts and Reports
Biologics Admin: Set Up Assays
Biologics Admin: Assay Grids
Biologics Admin: Service Request Tracker Set Up
Biologics Admin: URL Properties
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
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DataSpace: Plot Data
DataSpace: View Data Grid
DataSpace: Monoclonal Antibodies
Documentation Archive
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
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
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