/workshop-ncbi-data-with-python

Primary LanguagePython

Binder

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.