The various forms of biota

biota comes in 3 forms: a Python module, a command line function, and a Graphical User Interface (GUI). We recommend the use of the Python module for users with good knowledge of Python who wish to produce and adapt their own results. The command line form of biota is particularly adapted for batch jobs, and has been used to produce country-scale maps of biomass loss and probably deforestation with little scripting. Finally, the biota GUI provides an accessible tool for users who are less comfortable with scripting and terminals.

Using biota in Python

If your installation was successful, you should be able to import biota in Python:

import biota

You may now use biota in your Python scripts! See the worked examples to explore the different methods and attributes of biota in Python. Using biota in python will give you the most flexibility.

Using biota from the command line

For most applications, the command line interface will be the most straightforward way of using biota. It’s also the best way to run batch jobs.

To avoid having to reference the full path of the Python scripts in biota when using command line tools, add the following line to your .bashrc file:

alias biota='_biota() { python ~/full/path/to/biota/cli/"$1".py $(shift; echo "$@") ;}; _biota'

This creates a function that enables you to call biota just by typing biota in your terminal window. To run this function, restart your terminal or run bash (you will only need to do this once). You will then need to activate the biota environment once again.

Take a look at the worked examples to explore the possibilities when you using biota from the command line.

Using the biota Graphical User Interface (GUI)

The biota Graphical User Interface (GUI) allows you to use biota with minimal usage of the command line. In your terminal or the Anaconda prompt (if you’re using Windows), navigate to the folder where you installed biota by typing:

cd /full/path/to/biota/

This folder should have /biota/ at the end of its path. In this folder you will find a folder called Biota_app/. Navigate to it by typing:

cd Biota_app/

To open the GUI, type


The GUI window should then open. Now you can use biota several times with minimal typing.