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
      • 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
    • Systems Configuration
  • 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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  • Clowder (sensor data and computation management with web user interface)
  • Globus Connect (large data transfer)
  • BETYdb (phenotype data)
  • Algorithms (a.k.a. 'extractors')
  • Plant CV
  • Other Algorithms
  • Analysis Tools
  • CoGe
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Software

PreviousData SourcesNextScientific Objectives and Experimental Design

Last updated 7 years ago

TERRA-REF uses a suite of databases and software components that are described below.

Clowder (sensor data and computation management with web user interface)

Globus Connect (large data transfer)

BETYdb (phenotype data)

Algorithms (a.k.a. 'extractors')

Plant CV

Other Algorithms

Analysis Tools

CoGe

Clowder is the primary system used to organize, annotate, and process raw data generated by the phenotyping platforms as well as information about sensors. Use Clowder to explore the raw TERRA-REF data, perform exploratory analysis, and develop custom extractors. For more information, see .

Raw data is transferred to the primary TERRA-REF compute pipeline using Globus Online. Globus also provides access to TERRA REF files, but this is not a primary portal and metadata in Clowder may be required to locate and interpret these files. Use Globus Online when you want to transfer data from the TERRA-REF system for local analysis by accessing the . For more information, see .

BETYdb is a database and web interface to the trait / phenotype data and agronomic metadata. This is where you can find plant and plot level trait data as well as plot locations and other information associated with agronomic experimental design. Use BETYdb to access derived trait and agronomic data. For more information, see .

is an imaging processing package specific for plants that is built upon open-source software platforms , , and . Plant CV is used for trait identification, the output is stored in both Clowder and BETYdb.

Each step in the pipeline is performed by an algorithm. These are maintained in the TERRA REF GitHub organization in repositories with names that begin in extractors-* such as .

The NDS Workbench enables users to access the large filesystem and databases with familiar development environments. We provide a variety of environments for developing new algorithms and integrating them into the TERRA REF pipeline. These include and configured for specific use cases such as sensor data processing, trait analysis, database queries, and piepline development.

CoGe contains genomic information and sequence data. For more information, see .

Using Clowder
Terraref endpoint
Using Globus
Using BETYdb
Plant CV
OpenCV
NumPy
MatPlotLib
github.com/terraref/extractors-hyperspectral
RStudio
Jupyter Notebooks
Using CoGe