Under the GLOBE project, citizen scientists around the world have been monitoring mosquitoes. In particular, they have been counting larvae and attempting to identify the specific genera involved. This data is available from the GLOBE API. The goal of this notebook is to demonstrate how to download the data from the API using Python code, and how to create some useful visualizations. The hope is for this notebook to be both an exploratory tool of the data at hand, as well as to serve as a tutorial for analyzing the GLOBE data in general.
It is available for distribution in three different ways:
https://mybinder.org/v2/gh/IGES-Geospatial/globe-mosquitoes-notebook/HEAD?filepath=mosquitoes.ipynb
This link will open a copy of the notebook in your browser. It is hosted by a free service called MyBinder.org. The advantage is that the Python environment is already established for you. The disadvantage is that resources are limited, and so the connection is lost after 10 minutes of inactivity.
You may save any changes you made, even after the connection is lost, by clicking the leftmost cloud icon in the toolbar. You may then reopen using the above link (not by simply reloading the page, as it turns out), and import your saved changes with the rightmost cloud icon. Often this results in opening all the code blocks, which you may close with the eye icon in the toolbar.
Another way to access the notebook is to download a containerized version that packages all the requirements but allows you to host it yourself. This requires installing an application called Docker. You may do so at the following site:
https://www.docker.com/get-started
You will need to create a username and password to access the DockerHub. Install the application, launch it, and sign in. Open a Terminal window and login with:
docker login
Pull the notebook image from DockerHub with:
docker pull matthewbandel/mosquitoes:latest
Then start up the notebook with:
docker run -p 8888:8888 matthewbandel/mosquitoes:latest
You will get links to the browser looking something like this:
The Jupyter Notebook is running at:
http://cecb97358251:8888/?token=f418eb5ae31a84affd7b44e96926ab91521d8b1c96d51b9c
or http://127.0.0.1:8888/?token=f418eb5ae31a84affd7b44e96926ab91521d8b1c96d51b9c
The second link will open up the home page from which you may access the notebook by clicking on 'mosquitoes.ipynb.'
Save any changes you make under File menu, Save and Checkpoint. At the homepage, you may download the notebook, using the token given in the link above.
When starting a new session, you may reupload this saved copy to reinstate any changes you made.
Alternatively, if you already have a Python environment, you may work directly with a copy of the notebook, using these four files:
• mosquitoes.ipynb, the notebook itself
• requirements.txt, a list of Python modules required to run the code
• postBuild, a set of commands for activating notebook navigation features
• jupyter_notebook_config.py, a Python file with some configuration settings
• protocols.txt, a list of mosquito bundle protocols
If you’re on a Mac, you may follow these steps to install:
Assuming you are in a Terminal window in the same directory with these files, running:
pip install -r requirements.txt
Then running:
sh postBuild
will activate notebook navigation features. Running:
jupyter notebook
will fire up the Jupyter home page in your default browser. You should be able to click on mosquitoes.ipynb to open the notebook. You may click on “Save and Checkpoint” from the File menu to save any changes. Typing Control-C from Terminal will shut it down.
A sixth file:
• mosquitoes.py
is provided as a working copy of the notebook's python code.
Questions?
This was developed using Python version 3.6.5 on MacOS with Chrome as the browser. I am hoping it will install correctly on most versions of Python 3, and will run on most browsers, but this has by no means been rigorously tested yet. As with the first notebook, we are expecting some issues across browsers and platforms.
I’ve tried to put some tips in the “Notes on Navigation” section. Otherwise, feel free to direct any feedback, issues, or questions my way at [email protected]. Thank you so much!
• Matt