Introduction to NCBI Data with Python

Created by Daniel Rice and Peter Cooper, Spring 2021

Learning objectives:

In this workshop you will learn how to:

• Use Python programming to download, analyze, and visualize data.
• Use Jupyter to create data analysis 'lab notebooks' that make it easy to reproduce and share what you did.
• Find data that is relevant to your project using the new NCBI Datasets resource.
• Download NCBI sequence data and manipulate it with the BioPython package.

Materials:

We will be using The Littlest JupyterHub to serve Jupyter notebooks to a class of 30--50 students.

Resource usage:

• During BLAST memory usage spikes to 500 MB, stabilizes at 215 MB, as measured by Jupyter's usage log extension.
• The downloaded data takes up only 65K of storage.
• The repository itself is about 40MB, mostly in the bin directory that holds the blast and muscle binaries.

Instructions:

1. Start AWS instance with TLJH. Copy the tljh-setup.sh from this repo into the instances "User data" field.
2. Connect the instance to the ElasticIP
3. Wait ~10 min for the Hub to be set up.
4. Install SSL certificate and configure hub to use it
5. Log in by going to: https://jupyterhub01.ncbi.nlm.nih.gov/hub?next=%2Fuser-redirect%2Fgit-pull?repo%3Dhttps%253A%252F%252Fgithub.com%252Fncbi%252Fworkshop-ncbi-data-with-python%26branch%3Dmain%26urlpath%3Dtree%252Fworkshop-ncbi-data-with-python%252F
6. Configure jupyterhub by opening a terminal and running tljh-config.sh. Restart your server if it's running.
7. Add the students to the user accounts under: Control panel -> Admin -> Add users.
8. Send students to: https://jupyterhub01.ncbi.nlm.nih.gov/hub?next=%2Fuser-redirect%2Fgit-pull?repo%3Dhttps%253A%252F%252Fgithub.com%252Fncbi%252Fworkshop-ncbi-data-with-python%26branch%3Dmain%26urlpath%3Dtree%252Fworkshop-ncbi-data-with-python%252Fnotebooks%252Fworkshop.py

jupytext will automatically create the notebook from workshop.py

Recovering a broken notebook

If a student changes their notebook so it won't run and can't undo the changes:

• Rename the notebook by clicking on the title "workshop" at the very top of the page. It doesn't matter what name they choose.
• Click the workshop link again to download a fresh copy.