TERRA-REF Documentation
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  • Introduction
  • Data Sources
  • Software
  • Scientific Objectives and Experimental Design
    • Protocols
      • Controlled Environment Protocols
      • Manual Field Data Protocols
      • Phenotractor Protocols
      • Sensor Calibration
      • Template Protocol
      • UAV Protocols
    • Experimental Design
      • Experimental Design Danforth
        • Sorghum Lines Danforth
      • Experimental Design Genomics
        • Sorghum Lines Genomics Year 1
        • Sorghum Lines Genomics Year 1 (continued)
        • Sorghum Lines Genomics Year 2
      • Experimental Design MAC
  • User Manual
    • What Data is Available
    • Data Products
      • Environmental conditions
      • Fluorescence intensity imaging
      • Genomics data
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Multispectral imaging data
      • Meteorological data
      • Controlled Environment phenotype data
      • Point Cloud Data
    • How to Access Data
      • Using Clowder (Sensor and Genoomics data)
      • Using Globus (Sensor and Genomics data)
      • Using BETYdb (trait data, experimental metadata)
        • Accessing BETYdb via ArcMap and other GIS software
      • Using CoGe (Genomics)
      • Using CyVerse (Genomics)
      • Using Analysis Workbench (all data)
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
    • Release / reprocessing schedule
  • Technical Documentation
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Directory Structure
    • Data Storage
    • Data Transfer
    • Data Processing Pipeline
      • Geospatial Time Series Structure
    • Data Backup
    • Data Collection
    • Data Product Creation
      • Genomic Data
      • Hyperspectral Data
    • Quality Assurance and Quality Control
  • Developer Manual
    • Submitting data to Clowder
    • Submitting data to BETYdb
    • Submitting Data to CoGe
    • Developing Clowder Extractors
  • Tutorials
  • Appendix
    • Code of Conduct
    • Collaboration Tools
    • Glossary
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Tutorials

PreviousDeveloping Clowder ExtractorsNextAppendix

Last updated 5 years ago

We have developed a set of tutorials that aim to provide users with 'quick start' introductions to the range of different TERRA REF datasets. Tutorials for accessing trait data, sensor data, and genomics data are organized by directory ("traits", "sensors", and "genomics"). These can be found at .

Many of the tutorials can be run on your own computer with Python or R installed. However, some require access to the filesystem or databases that can not be made public. To 'easiest' (guaranteed easier than collecting the data yourself!) place to start is on the terraref workbench, which provides all of the software dependencies and access to all of the data.

Data Access

Before using the tutorials, you should , agree to the data use policies and caveats about data access and quality.

Workbench

The tutorals are developed for use with the TERRA REF workbench (). The workbench provides two key features:

  1. access to large datasets on the filesystem and access to query the trait database

  2. pre-configured programming environments (Rstudio, Cloud9, Jupyter) that include software dependencies pre-installed.

The workbench uses Docker "Containers". In theory, anything you can run on Ubuntu can be deployed in workbench. The workbench by default includes the Docker Containers defined in the repository. If you want to use software that is not currently available on the toolserver you either suggest a change to one of the docker files, request new programs or libraries to be added, or explore the diversity of pre-configured containers in the .The on Docker Hub includes both the Workbench environments as well as the pipeline components.

terraref.org/tutorials
sign up for the early access program
https://www.workbench.terraref.org
terraref/toolserver-dockerfiles
Docker Store
TERRA REF organization