Python Study Group

The Jackson Laboratory

Dec 4, 6, 11, 13, 18, & 20, 2019

11:00 am - 12:00 pm

Instructors: Participants take turns presenting exercises and solutions

General Information

This Python study group will explore the Pandas (short for panel data) library. Pandas aims to close the gap in the richness of data analysis tools in Python and the numerous domain-specific statistical computing platforms and database languages. We’ll study chapter 4 of Jake VanderPlas’ Python Data Science Handbook on our own time, then challenge each other with exercises during twice-weekly one-hour meetings. For more information and a schedule, please visit the workshop website.

Prerequisite: Software Carpentry’s Plotting & Programming in Python, or Python competence gained otherwise.

We will meet via WebEx. If you’d like to join the group in person, you can meet in:

Bar Harbor at the The Oasis

Farmington at the Helix Café

This is open to those at JAX and elsewhere who have the prerequisite Python skills.

Where: online. Get directions with OpenStreetMap or Google Maps.

When: Dec 4, 6, 11, 13, 18, & 20, 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.) and must install WebEx if attending via web conference. 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.

Schedule

Wednesday, Dec 4

11:00 Welcome and introductions
11:15 Introducing Pandas Objects: Group exercises
11:30 Data Indexing and Selection: Group exercises
12:00 END

Friday, Dec 6

11:00 Operating on Data in Pandas: Group exercises
11:30 Handling Missing Data: Group exercises
12:00 END

Wednesday, Dec 11

11:00 Hierarchical Indexing: Group exercises
11:30 Combining Datasets: Concat and Append: Group exercises
12:00 END

Friday, Dec 13

11:15 Combining Datasets: Merge and Join: Group exercises
11:30 Aggregation and Grouping: Group exercises
12:00 END

Wednesday, Dec 18

11:00 Pivot Tables: Group exercises
11:30 Vectorized String Operations: Group exercises
12:00 END

Friday, Dec 20

11:15 Working with Time Series: Group exercises
11:30 AHigh-Performance Pandas: Group exercises
12:00 END

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

Syllabus

Data Manipulation with Pandas

  • Installing and Using Pandas
  • Pandas Objects
  • Data Selection in Pandas Objects
  • The Pandas Index Object
  • Universal Functions
  • Combining Datasets
  • High-Performance Pandas
  • 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.