# 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](http://terraref.ncsa.illinois.edu/clowder/spaces) or [API](https://terraref.ncsa.illinois.edu/clowder/assets/docs/api/index.html).

See the [Clowder documentation](https://clowder.ncsa.illinois.edu/docs/) for more information about the software and its applications.

## Requesting Access

To create an account, sign up at the [TERRA-REF Clowder site](https://terraref.ncsa.illinois.edu/clowder/spaces) 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](https://opensource.ncsa.illinois.edu/confluence/display/CATS/Extractor+Development) documentation


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