Shafaq Chaudhry, Mark Durbin, Carlos Acevdeo, Ezequiel Gioia
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 and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
The best way to learn how to program is to do something useful,
so this introduction to Python is built around a common scientific task: data analysis.
We are studying inflammation in patients who have been given a new treatment for arthritis,
and need to analyze the first dozen data sets of their daily inflammation.
The data sets are stored in comma-separated values (CSV) format.
We will learn to do basic operations such reading data from files,
processing & analyzing the data, generating plots, and automating tasks.
The course is aimed at graduate students and other researchers.
This is a basics level workshop for an audience who intend to start working with Python in the future.
You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: This training will take place online via Zoom. Once you register for the workshop,
you will recieve Zoom meeting details with other important information and instructions via email.
Participants must have access to a computer 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).
We are dedicated to providing a positive and accessible learning environment for all. Please
notify the instructors in advance of the workshop if you require any accommodations or if there is
anything we can do to make this workshop more accessible to you.
If you haven't used Zoom before, go to the
to download and install the Zoom client for your computer.
Set up your workspace
Like other Carpentries workshops,
you will be learning by "coding along" with the Instructors.
To do this, you will need to have both the window for the tool
you will be learning about (a terminal, RStudio, your web browser, etc..)
and the window for the Zoom video conference client open.
In order to see both at once,
we recommend using one of the following set up options:
Two monitors: If you have two monitors,
plan to have the tool you are learing up on one monitor and
the video conferencing software on the other.
Two devices: If you don't have two monitors,
do you have another device (tablet, smartphone) with a medium to large
sized screen? If so, try using the smaller device as your video
conference connection and your larger device (laptop or desktop)
to follow along with the tool you will be learning about.
Divide your screen: If you only have one device
and one screen, practice having two windows
(the video conference program and one of the tools you will be using
at the workshop) open together.
How can you best fit both on your screen?
Will it work better for you to toggle between them
using a keyboard shortcut?
Try it out in advance to decide what will work best for you.
This blog post includes detailed information on how to set up your screen to follow along during the workshop.
Python is a popular language for
research computing, and great for general-purpose programming as well.
We will teach Python using the Jupyter Notebook;
a programming environment that runs in a web browser. For the workshop, we will provide you
with a JupyterHub server where you will be able to login and perform your coding tasks on a Jupyter Notebook.
If you wish to install tools on your own system, then note that Jupyter Notebook can be installed using Anaconda.
Installing all of its research packages individually can be a bit difficult, so that is why we recommend
Anaconda, an all-in-one installer.
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
(some older browsers, including Internet Explorer version 9
and below, are not).
You can also install Python without Anaconda.
Also, you can also work with Python without using Jupyter Notebook.
You will need to install Python and a programmer-friendly code editor.
Regardless of how you choose to install it,
please make sure you install Python version 3.x
(e.g., 3.6 is fine).
Download the Anaconda Installer with Python 3 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.)
Open a terminal window and navigate to the directory where
the executable is downloaded (e.g., `cd ~/Downloads`).
and then press
Tab to autocomplete the full file name. The name of
file you just downloaded should appear.
(or Return depending on your keyboard).
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 (or Return)
to approve the default location
for the files.
Type yes and press
Enter (or Return)
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).