Intermediate Python: Programming

URL to this page: https://hackmd.io/@k8hertweck/PythonProgramming

This page is for easy access to links we'll use during class. You don't need to do anything with this information until directed by your instructor. Links to the instructor's script will be added as the course progresses.

Sign in to each class meeting here

You should have Python installed on your computer, as well as a preferred interface for writing Python code. You can view some recommendations here. Your instructor will be using Jupyter notebooks for this course.

Complete class notes here

If you have feedback about this course, please comment here

Special note: Tomorrow there has been a request to #ShutDownAcademia and #ShutDownStem. We acknowledge that much of the work we do at the Hutch is time-sensitive, so we will still hold class. However, we support anyone who may choose to participate in the shutdown. If that is the case, please message your instructor if you would like to set up a meeting before the next class to review any questions you might have.

Class 1

• Today's materials
• URL for data: http://swcarpentry.github.io/python-novice-inflammation/data/python-novice-inflammation-data.zip
• About Python interpreters
  • Blog post comparing VS Code, PyCharm, and Jupyter Notebooks
  • VS Code keyboard shortcuts for Windows
• Other useful info:
  • Essential built-in Python functions blog post

Class 2

• Today's materials
• Packages (libraries) are collections of functions related to specific types of work in Python, and are often contributed by members of the community. Some of the most popular packages include:
  • pandas: data analysis (data science)
  • numpy: numerical python (a part of scipy)
  • biopython: biological computation, including sequence analysis

Class 3

• Today's materials

Class 4

• Today's materials
• Resources for more Python learning:
  • Coop Community Slack has a python channel (#python-user-comm) that is a great resource for troubleshooting and learning how people at the Hutch work with python
  • Biomedical Data Science Wiki has a python page with info about accessing other python tools at fred hutch
  • There are a number of Python groups in the greater Seattle area available through meetup. This includes groups specific to certain topics, as well as groups focused on certain demographics (e.g., PyLadies)

Resources for continued learning

• Learn about other courses through fredhutch.io here
• The Fred Hutch Bioinformatics and Data Science Cooperative, or Coop, hosts many community meetings and office hours about data science. Learn more information about these groups here
• Join the Coop Community Slack to talk about data science with other Hutch researchers!
• The Fred Hutch Biomedical Data Science Wiki is written by Hutch researchers and staff, and is a great place to find information about data management, bioinformatics, computing, and more.

tags: fredhutch.io python