Plotting and Programming with Python

Jan 30-31, 2019

9:00 am - 4:30 pm

Instructors: Sheldon McKay, Sue McClatchy, David McKenzie, Sandeep Namburi, Pariksheet Nanda

Helpers: Samir Amin, Ravi Pandey

General Information

Where: The Jackson Laboratory for Genomic Medicine, Holt Conference Rooms 1405 & 1410, 10 Discovery Drive, Farmington, Connecticut. Get directions with OpenStreetMap or Google Maps.

When: Jan 30-31, 2019. 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 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 for more information.


Wednesday, January 30

09:00 Workshop Overview
09:30 Running and Quitting
09:45 Variables and Assignment
10:05 Data Types and Type Conversion
10:30 Coffee
10:45 Built-in Functions and Help
11:15 Libraries
12:05 Reading Tabular Data into DataFrames
12:30 Lunch break
13:30 Pandas DataFrames
14:15 Plotting
15:00 Coffee
15:15 Lists
15:45 For Loops
16:15 Wrap-up

Thursday, January 31

09:00 Looping Over Data Sets
09:30 Writing Functions
10:30 Coffee
10:45 Variable Scope
11:15 Conditionals
11:45 Programming Style
12:15 Wrap-up
12:30 End

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


Programming in Python


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

We maintain a list of common issues that occur during installation as a reference for instructors 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 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 Add Anaconda to my PATH environment variable.


Video Tutorial
  1. Open 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 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 Return. You will follow the text-only prompts. To move through the text, press Spacebar. 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.