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2024-APR-05: Interactive workshop on Git & Python for Reproducible Research

Workshop teaser

• To see how to recreate a web app based on Streamlit and more!

Setup

April 4th - prep session

• We will assist attendees with installing Anaconda3 and getting accounts for Streamlit and GitHub.

April 5th - main session

Please create an account for each of the following platforms depending on your personal goals:

Accounts to obtain	Goals
Colab	... if you would like to save your work done during the workshop
Colab, GitHub, Streamlit	... if you would like to get the most out of the workshop
Colab, GitHub, Streamlit, Kaggle	... if you would like to try out everything that was mentioned during the workshop

Colab + Kaggle offer free Graphical Processing Units for your deep learning applications.

Quick how-to

• Windows users, visit Citrix PHSA login page to download Anaconda3 (needed for creation of virtual environments)
• Mac users, use terminal and simply copy-paste to install Git:

  /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  brew install git
  

Python from beginning

Complexity
Python 101	- Colab notebooks on select topics to help you get started <-- Offers free GPU - https://ubc.syzygy.ca/ - https://sfu.syzygy.ca/ - Jupyter.org
Python 102	- Installing on your personal device with admin rights - Creating virtual environments inhouse - Guidelines - IDE tools
Python 201	- Demo on writing classes - Demo on Copying objects
Python users picking up R	- 2019 blog

For software-production projects, please consult with your manager before electing to develop your products in Python.

R users complementing work with Python

• Resources

Reproducible Research (RR)

• Resources
• Repeatable development environments with IDE

Open textbooks

• R for Data Science (Python version)
• Python for SAS Users
• Introduction to Statistical Learning

  • Python / R versions of this textbook

    Setting up the virtual environment for ISLP

    To install the current version of the requirements run:

    $ pip install -r https://raw.githubusercontent.com/intro-stat-learning/ISLP_labs/v2.1.3/requirements.txt
    $ jupyter lab Ch02-statlearning-lab.ipynb   # an example to launch the notebook for Chapter 2 
    

Domain specific

• Python for biologists

Workshop developers & facilitators

• Ying Tang
• Afraz Khan
• Nirupama Tamvada

Acknowledgements

Many thanks to Data & Analytics Services and the curriculum consultants:

• Abdulaa Babili
• Chris Fjell
• Citlali Marquez
• Dahn Jeong
• Fran Thistlethwaite
• Jamal Taghavimehr
• John Palmer
• Michael Kuo
• Mike Irvine
• Rebeca Falcao

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Shield:

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.