# Software

TERRA-REF uses a suite of databases and software components to automate the analysis of sensor data to produce plant and plot level traits / phenotypes, store and provide access to data..

![](/files/-LBSUWUl9M50oJQT1Qxu)

## Databases

### 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](broken://pages/-LBSUWCJYDv6ndBW6c6k).

### Globus Connect (large data transfer)

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 [Terraref endpoint](https://www.globus.org/app/endpoints/403204c4-6004-11e6-8316-22000b97daec/overview). For more information, see [Using Globus](broken://pages/-LBSUWCK0POrzXf_RJtC).

### **BETYdb (phenotype data)**

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 [Using BETYdb](broken://pages/-LBSUWCLbasAB1SkMMO7).

## Algorithms

### Extractors

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 [github.com/terraref/extractors-hyperspectral](https://github.com/terraref/extractors-hyperspectral).

### Plant CV

[Plant CV](http://plantcv.danforthcenter.org/) is an imaging processing package specific for plants that is built upon open-source software platforms [OpenCV](http://opencv.org/), [NumPy](http://www.numpy.org/), and [MatPlotLib](http://matplotlib.org/). Plant CV is used for trait identification, the output is stored in both Clowder and BETYdb.

### **CoGe**

[*CoGe*](https://genomevolution.org/coge/) is a platform for performing Comparative Genomics research. It provides an open-ended network of interconnected tools to manage, analyze, and visualize next-gen data. CoGe contains genomic information and sequence data from the TERRA REF project. 


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