Plotting and Programming in Python

Oct 16, 23, and 30, 2019

1:00 pm - 4:30 pm

Instructors: Sue McClatchy, Luis Sordo Viera, Susan Sheehan, Bill Flynn, Daniel Danis, Neil Kindlon, Olaitan Awe

Helpers: Andrew Deighan, Asli Uyar, Sirohi Kumar

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers at JAX and nearby institutions. You can attend from either the Bar Harbor or Farmington campus. Please plan to be physically located in the same room with other participants. We don’t allow individual participants to attend remotely because we provide support, and we can’t do that if you’re not here in the room with us. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: The Jackson Laboratory, Breezeway Bioinformatics Training Room, 600 Main Street, Bar Harbor ME | The Jackson Laboratory for Genomic Medicine, Room 4320, 10 Discovery Drive, Farmington CT. Get directions with OpenStreetMap or Google Maps.

When: Oct 16, 23, and 30, 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.). They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

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 susan.mcclatchy@jax.org for more information.

Surveys

Please be sure to complete these surveys before and after the workshop.

Schedule

Wednesday, Oct 16

Before Pre-workshop survey
13:00 Welcome and introductions
13:15 Running and Quitting
13:40 Variables and Assignment
13:00 Data Types and Type Conversion
14:45 Afternoon break
15:00 Built-in Functions and Help
15:40 Libraries
16:25 Wrap-up
16:30 END

Wednesday, Oct 23

13:00 Reading Tabular Data into DataFrames
13:45 Pandas DataFrames
14:45 Afternoon break
15:00 Plotting
15:40 Lists
16:25 Wrap-up
16:30 END

Wednesday, Oct 30

13:00 For Loops
13:30 Looping Over Data Sets
14:00 Writing Functions
14:45 Afternoon break
15:00 Variable Scope
15:30 Conditionals
16:00 Programming Style
16:15 Post-workshop Survey
16:30 END

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

Syllabus

Programming in Python

  • Using Libraries
  • Working with Arrays
  • Reading and Plotting Data
  • Creating and Using Functions
  • Loops and Conditionals
  • Defensive Programming
  • Reference...

Setup

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

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).

  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 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.