May 18 & 19, 2017
McMaster University, Hamilton Hall room 102
Instructors: Ben Bolker, Jake Cowper Szamosi
Helpers: Jennifer Stearns, Ben Furman, Fiona Whelan, Sharok Shekarriz, Jonathan Dushoff
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 the Unix shell, version control, data management in R, 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, post-docs, staff, and PIs who want to improve their informatics skills. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
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 read and abide by Software Carpentry's Code of Conduct.
We expect all participants to come with needed software installed. If you have trouble, or would like help with, installing any of the software, please attend our software installation party, May 16 at 4pm in LSB 216.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop; please notify the organizers in advance if you need large-print handouts.
Contact: Please email Jake at firstname.lastname@example.org for more information.
Enrollment in this workshop must be done in advance and costs $20. You can sign up on Eventbrite. We encourage PIs to cover the cost of the workshop for their trainees out of grants wherever possible. If payment by credit card/p-card is not possible, please email us to arrange to pay with a grant number.
Please be sure to complete these surveys before and after the workshop.
.zipfiles (e.g. by right-clicking/control-clicking and selecting "Save Link As ...") and unzip them somewhere appropriate (e.g., in your Desktop).
|09:00||Automating tasks with the Unix shell (Ben)|
|10:45||More automating tasks with the Unix shell (Jake)|
|13:00||Programming with R (Ben: Analyzing patient data, Creating functions)|
|14:30||More Programming with R (Jake: Analyzing multiple data sets, Making choices, Best practices, Intro to RStudio)|
|09:00||Version control with Git (Jake)|
|10:45||More version control with Git (Ben)|
|13:00||Back to Programming with R (Jake: addressing data, reading & writing CSV files, looping)|
|14:35||End with Programming with R (Ben: understanding factors, data frame manipulation with dplyr, rearranging data with tidyr (if time))|
To participate in a Software Carpentry 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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmdand press [Enter])
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen pressing [Enter]
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing
bash. There is no need to
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo yum install git.
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on Mac OS X and
Linux is usually set to Vim, which is not famous for being
intuitive. if you accidentally find yourself stuck in it ("beep mode"),
try typing the escape key, followed by
:q! (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.
We will use the Atom editor in this workshop. The Atom installation page gives simple downloading and installation instructions for all three operating systems (you should be directed to the page with instructions for your OS; if not, click on the appropriate link in the upper right of the window).
If you are unable to install the Atom editor, you can use one of these alternative text editors:
If you have previously installed R and/or RStudio, please make sure if at all possible that you have the most up-to-date versions. If your current R version is 3.2.5 or older, you will need to re-install packages and will get the latest versions of all packages by default; please be careful if you depend on a particular release of a package. Feel free to contact the organizers if you have any concerns.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Once you've installed R and RStudio, launch RStudio, go
to the console and
packages by typing
install.packages("dplyr") install.packages("tidyr")(while you are connected to the Internet). If this is giving you prolems on Windows, try restarting R by right clicking and choosing "run R as administrator."