Feb 10-11, 2018
8:30 am - 4:30 pm
Instructors: Marnee Dearman, Benjamin J. Hickson, Uwe Hilgert, Andreina C. Siri, Brian A. Smith
Helpers: Shu Cheng, Dawson Fairbanks, Xiao Feng, Manoj Gopale, Monique Lassere, Lolita Mathew, Jeanine McGann, Xue Pan, Travis Struck, Dhiraj Thakare
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. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: Drachman Hall B109, UA.
When: Feb 10-11, 2018. Add to your Google Calendar.
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 abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Links to workshop materials are being provided below. If we can provide additional resources to help making learning easier for you (e.g. large-font hand-outs, sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email email@example.com for more information.
Please be sure to complete these surveys before and after the workshop, respectively.
|08:30||Access and navigate the command line / Bash Shell|
|10:45||Manage data with git/GitHub|
|13:00||Automate tasks with shell scripts|
|15:00||Share data and scripts/programs with git/GitHub|
|17:00||End of Day|
|08:30||Analyze scientific data with Python and git/GitHub|
|11:00||Analyze scientific data with Python and git/GitHub, cont.|
|13:00||Analyze scientific data with Python and git/GitHub, cont.|
|15:00||Analyze scientific data with Python and git/GitHub, cont.|
|17:00||End of Day|
Schedule subject to change if necessary.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Find, create, copy, move and delete folders and files
Syllabus subject to change if necessary.
To participate in a Software Carpentry workshop, you will need access to the software described below. Unless you prepare your laptop as described below you will be unable to follow along. In addition, you will need an up-to-date web browser, we recommend Firefox, Chrome or Safari as Internet Explorer can be buggy.
Should you encounter issues while installing the software below, please look for a solution in our Configuration Problems and Solutions wiki page. If even this does not help, please get in touch (using contact details above) and we will attempt to provide a solution.
Bash is a commonly-used shell (= Unix command language) that gives you the power to quickly do simple tasks on your computer. Bash stands for 'Bourne Again Shell'; if you are interested in the history of the term and the underlying technological development, please search the Web for 'Bash Shell'.
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 macOS 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 dnf install git.
Writing code is much easier with respectively optimized text editors that include features such as automatic color-coding of key words and syntax-highlighting. We will use the basic editor 'nano' in the workshop; it comes pre-installed with the git-bash download above for Windows, Mac and Linux.
Click the Start button and type 'nano' into the search window. If your computer is unable to locate nano, install it by downloading/saving the Software Carpentry Windows installer. Double-click the installer file to run it. (CAVEAT: This installer requires an active internet connection.)
During the workshop we will be using the basic editor nano. nano should be pre-installed; see the Git installation video tutorial for an example on how to open nano.
During the workshop we will be using the basic editor nano. nano should be pre-installed
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).
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 DownloadsThen, try again.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).