Yale University Library

April 18, 2018

1:00 pm - 5:00 pm

Instructors: Catherine DeRose, Joshua Dull, Kate Nyhan

General Information

This workshop is adapted from materials developed by Software Carpentry.

This hands-on workshop will cover basic concepts and tools, including program design and task automation in Python. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at graduate students and other researchers, but open to all members of the Yale community (students, faculty, and staff). You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room 118A, Center for Teaching & Learning, 301 York St, New Haven, CT 06511. Get directions with OpenStreetMap or Google Maps.

When: April 18, 2018. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email catherine.derose@yale.edu , joshua.dull@yale.edu or kate.nyhan@yale.edu for more information.


April 18th

1:00 pm Introductions & Logistics
1:20 pm Analyzing Data
1:50 pm Break
2:00 pm Repeating Actions with Loops
2:30 pm Storing Multiple Value in Lists
3:00 pm Break
3:10 pm Analyzing Data from Multiple Files
3:30 pm Making Choices
4:00 pm Break
4:10 pm Creating Functions
4:40 pm Errors, Debugging, and Wrap-up
5:00 pm END

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Workshop Etherpad

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...


To participate in this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

Software Carpentry maintains a list of common issues that occur during installation that may be useful on the Configuration Problems and Solutions wiki page.


Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).


Video Tutorial
  1. Open https://www.anaconda.com/download/#windows with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.


Video Tutorial
  1. Open https://www.anaconda.com/download/#macos with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.


  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
    cd Downloads
    Then, try again.
  5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.


In preparation for this lesson, you will need to download two zipped files and place them in the specified folder:

  1. Make a new folder in your Desktop called `python-novice-inflammation`.
  2. Download python-novice-inflammation-data.zip and move the file to this folder.
  3. Also download python-novice-inflammation-code.zip and move it to the same folder.
  4. If the files aren't unzipped yet, double-click to unzip them. You should end up with two new folders called `data` and `code`.

Jupyter Notebook

To start the notebook server, open a terminal or git bash and execute the command: 'jupyter notebook'. Then create a new notebook using the drop-down menu on the right to select 'Python 3 notebook'.