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.
Who:
The course is aimed at graduate students and other researchers.
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).
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:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
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.
First and foremost, we recommend the lessons from Software Carpentry that we followed for this course. We've added links to those lessons in the syllabus above.
Downloadable etherpad notes (Right click and choose save-as): HTML, PDF, Word Doc.
Programming & Data Analysis with R
General R Help
rdrr.io: Nicely formatted help for functions in R packages. Easier to read and even lets you run examples in your browser!
RStudio Cheatsheets: Especially recommend data wrangling, data visualization, and R markdown.
stackoverflow.com: Great place to ask for or search for help with specific problems. Many package authors monitor this website.
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.
Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.
Select "Use the nano editor by default" and click on "Next".
Keep "Git from the command line and also from 3rd-party software" selected and click on "Next".
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.
Click on "Next".
Select "Use the native Windows Secure Channel library", and click "Next".
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
Select "Use Windows' default console window" and click on "Next".
Leave all three items selected, and click on "Next".
Do not select the experimental option. Click "Install".
Click on "Finish".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing [Enter]
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities).
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
install anything.
Git
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.
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.
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your /Applications folder,
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"
available here.
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 dnf install git.
Text Editor
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 macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+Q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
Others editors that you can use are
Notepad++ or
Sublime Text.
Be aware that you must
add its installation directory to your system path.
Please ask your instructor to help you do this.
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.
R is a programming language
that is especially powerful for data exploration, visualization, and
statistical analysis. To interact with R, we use
RStudio.
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.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo dnf install R). Also, please install the
RStudio IDE.