Software

TERRA-REF uses the following software.

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

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 Using Clowder.

Globus Connect (large data transfer)

Raw data is transferred to the primary TERRA-REF compute pipeline using Globus Online. Data is available for Globus transfer via the Terraref endpoint. Use Globus Online when you want to transfer data from the TERRA-REF system for local analysis. For more information, see Using Globus.

BETYdb (phenotype data)

BETYdb contains the phenotype data with plot locations and other information associated with agronomic experimental design Use BETYdb to access derived trait and agronomic data. For more information, see Using BETYdb.

Plant CV

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

Analysis Tools

The Clowder system supports launching external analysis environments such as RStudio and Jupyter Notebooks for anlaysis.

CoGe

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

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