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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  • About Clowder
  • Requesting Access
  • Data organization
  • Searching the database
  • Analyzing data in Clowder
  • Clowder Extractors
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  1. User Manual
  2. How to Access Data

Using Clowder (Sensor and Genoomics data)

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Last updated 7 years ago

About Clowder

Clowder is an active data repository designed to enable collaboration around a set of shared datasets. TERRAREF uses Clowder to organize, annotate, and process data generated by phenotyping platforms. Datafiles are available via the Clowder or .

See the for more information about the software and its applications.

Requesting Access

To create an account, sign up at the and wait for your account to be approved. Once access is granted, you can explore collections and datasets.

Data organization

Data is organized into spaces, collections, and datasets, collections.

  • Spaces contain collections and datasets. TERRA-REF uses one space for each of the phenotyping platforms.

  • Collections consist of one or more datasets. TERRA-REF collections are organized by acquisition date and sensor. Users can also create their own collections.

  • Datasets consist of one or more files with associated metadata collected by one sensor at one time point. Users can annotate, download, and use these sensor datasets.

Searching the database

Clowder allows users to search metadata and filter datasets and files with particular attributes. Simply enter your search terms in the search box.

Analyzing data in Clowder

Clowder includes support for launching integrated analysis environments from your browser, including RStudio and Jupyter Notebooks.

After selecting a dataset, under the "Analysis Environment Instances", select the "Launch new instance with dataset" drop-down, select the desired tool, then the "Launch" button. Select the "Environment manager" link to view the list of active instances. Find your instance and select the title link. This will display the tool with the selected dataset mounted. If you have a running instance, you can also "Upload dataset to existing instance".

Clowder Extractors

Through it's extractor architecture, Clowder supports automated computational workflows. For more information about developing Clowder extractors, see the documentation

web interface
API
Clowder documentation
TERRA-REF Clowder site
Extractor Development