This folder contains some example notebooks that can be used in Leonardo. These notebooks are purely for demo purposes; they do not contain any sensitive data.
To try out an example notebook, download it to your machine, open Jupyter, and select Upload.
Here is a current listing of example notebooks. Please keep this up to date if you add more.
- Hail_Tutorial.ipynb
- Contains the Hail 0.1 (stable) tutorial, adapted from here: https://hail.is/docs/stable/tutorials/hail-overview.html
- LeonarDemo.ipynb
- Python 2 sample notebook which loads the FireCloud data model into pandas objects, interacts with Google Cloud Storage APIs, and runs a basic Hail job.
- NOTE: references a demo workspace which no longer exists, so won't be runnable as-is.
- Python 2 sample notebook which loads the FireCloud data model into pandas objects, interacts with Google Cloud Storage APIs, and runs a basic Hail job.
- Notebooks_Demo_Manning_Lab.ipynb
- Python 2 notebook which runs an analysis of publicly available 1000 genomes data. Uses FISS for interacting with a FireCloud workspace and pandas and numpy for manipulating data. Runs Hail 0.1 to do some analysis.
- Developed by Alisa Manning's team for demonstration purposes.
- Safari_Online_Jupyter_Training.ipynb
- Adaptation of Safari online Jupyter training which exercises some basic tools like pandas, numpy, and matplotlib in Python 3.
NEEDED: example notebook using R and bigquery.