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Tutorials

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Tutorials

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These tutorials provide an "hands on" introduction to the core features of LabKey Server, giving step-by-step instructions for building solutions to common problems.

They are listed roughly from simple to more complex. You can start with the New User tutorials, or you can start with a tutorial further down the list that interests you.

  New User Tutorials

 Data Grid Tour
 Take a quick tour through LabKey Server.		  • Data grids and visualizations  • tutorial  
 Security 
 Learn how to organize and secure your data using
 LabKey Server.		  • Project and folder organization
 • Customize look and feel
 • Security and user groups		  • tutorial
 File Sharing
 Manage, search, and share file resources. 		 • Import and manage data files
 • Search data
 • Share data files		  • tutorial
 Collaboration Tools
 Learn how to use LabKey Server's secure,
 web-based collaboration tools.		  • Set up message boards and announcements
 • Provide contextual content using a wiki
 • Manage team tasks with a shared issue tracker		  • tutorial
 List
 Explore list data structures.		  • Use and connect lists
 • Add lookups and URL properties
  • tutorial
 Electronic Lab Notebook
 Learn how set up a basic ELN.		  • Capture sample and assay data
 • Connect data in different tables
 • Refine user interface and link navigation		  • tutorial

  Study Tutorials

 Study Features
 Integrate and analyze observational study data
 and assay/mechanistic data.		  • Discover data trends; compare cohorts
 • Integrate heterogeneous data 
 • Visualize data in time charts		  • tutorial

 Set Up a New Study
 Create a new observational study from scratch.

  • Create and configure a new Study
 • Integrate heterogeneous datasets
 • Set up specimen management
 • Use your own data or provided sample data		  • tutorial
 Specimen Repository Management
 (for Admins)		  • Set up a specimen repository and request system   • tutorial
 Use the Specimen Repository
 (for Specimen Requesters)		  • Browse and request specimen vials with an online shopping cart    • tutorial

  Assay Tutorials

 Introduction to Assay Tools
 How to import, manage, and integrate assay
 data into an observational study.

  • Design instrument-specific tables for your assay data
 • Import run data to an assay design
 • Perform quality control tests on data
 • Add data to a pre-existing study		  • tutorial

 NAb (Neutralizing Antibody) Assay
 Work NAb experiment data from 96-well or
 384-well plates.

  • Create a design/model for the NAb plate
 • Examine results and curve fit options		  • tutorial
 • interactive example

 ELISA Assay
 Import and analyze ELISA experiment data. 

  • Set up ELISA plate templates
 • Import ELISA assay data
 • Visualize and analyze the data		  • tutorial

 ELISpot Assay
 Import and analyze ELISpot experiment data. 

  • Configure an ELISpot plate template
 • Create designs based on the configured template
 • Import and analyze data 		  • tutorial
 • interactive example
 Proteomics (CPAS)
 Storage and analysis for high-throughput
 proteomics and tandem mass spec experiments.		  • Import and annotate MS2 data
 • Analyze data with X! Tandem, Peptide/ProteinProphet
 • Build custom data grids and reports		  • tutorial
 Flow Cytometry: Basics
 Set up a repository for management, analysis, and
 high-throughput processing of flow data.		  • Set up a flow dashboard
 • Import data from FCS files and FlowJo
 • Build custom grids of imported data		  • tutorial
 • interactive example

 Flow Cytometry: Flow Analysis  
 Analyze flow data.

  • Define a Compensation Calculation
 • Calculate statistics using the LabKey Flow engine		  • tutorial
 • interactive example

 Luminex: Level I
 Manage, quality control, analyze, share, integrate
 and export Luminex immunoassay results.

  • Import Luminex assay data
 • Collect pre-defined analyte, run and batch properties
 • Exclude an analyte's results from assay results
 • Import several files of results together		  • tutorial
 • interactive example

 Luminex: Level II 
 Use advanced features for quality control and
 analysis.

 • View curve fits and calculated values for each titration
 • Visualize performance using Levey-Jennings plots
 • Determine expected ranges for performance of standards
 • Flag exceptional values

  • tutorial
 • interactive example

 Microarray 
 Work with sample microarray data.

 • Upload data from MAGE-ML data files
 • Create a microarray assay design

  • tutorial
 • interactive example

 Expression Matrix 
 Try an example expression matrix assay.

 • Tie expression data to sample and feature/probe information
 • Work with Gene Expression Omnibus (GEO) data

  • tutorial

  Developer Tutorials

 JavaScript Client API: Build a
 Reagent Request System		  • Create a reagent request tracking system
 • Visualize reagent request history
 • Optimize reagent fulfillment system		  • tutorial       
 • interactive example
 JavaScript Client API: URLs, Filters,
 Passing Data Between Pages		  • Pass parameters between pages via a URL
 • Filter a grid using a received URL parameter		  • tutorial
 Export Chart as JavaScript  • Work with JavaScript directly to customize a visualization   • tutorial
 JavaScript Charts  • Create custom visualizations in JavaScript  • tutorial
 Modules: Queries, Views and Reports  • Develop file-based queries, views, and reports in a module
 • Encapsulate functionality in a module		  • tutorial
 Hello World Module  • Develop file-based views.
 • Encapsulate functionality in a module		  • tutorial
 Workflow Module
 Incorporate business process management workflows.		  • Install and use a sample workflow
 • Customize workflow process definitions
  • tutorial
 Assay Module  • Create custom assay design and user interface 
 • Encapsulate functionality in a module		  • tutorial
 Extract-Transform-Load Module
 Create and use a simple ETL.		  • Extract data into LabKey programattically
 • Clean or reshape data with transform scripts
  • tutorial

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