Using Clowder (Sensor and Genoomics data)

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 web interface or API.

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

Requesting Access

To create an account, sign up at the TERRA-REF Clowder site 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 Extractor Development documentation