June 8-9, 2016
8:30 am - 4:00 pm
Instructors: Matt Garcia, Lauren Michael, Danielle Nielsen, Sarah Stevens
Helpers: Karl Broman, Ethan Nelson, Andy Pohl
Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. 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 researchers who have no prior experience with programming and just want to get started in some basic skills for organizing, combining, and visualizing data, our UW-Madison Data Carpentry workshop (June 1-2) will likely be more appropriate. These two workshops are NOT intended to be taken back-to-back, and you can learn about future workshops at UW-Madison by joining the mailing list of UW-Madison's Advanced Computing Initiative.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at UW-Madison graduate students and other UW-Madison researchers. Some prior experience with programming is strongly recommended.
Requirements: Participants must be affiliated with UW-Madison and bring a laptop with a few specific software packages installed (listed below). An individual should only register if he/she is able to attend ALL days of the workshop. While coffee and tea will be provided, participants should eat a full breakfast and plan to bring or buy their own lunch nearby. Attendees are also required to abide by Software Carpentry's Code of Conduct. Registration is required, and will be available just above General Information, starting at 5:00 pm on Wednesday, May 4.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
If we can help making learning easier for you or you have any concerns, please contact us preferably by August 15, so that we have time to respond before the workshop.
Contact: Please mail ContactACI@lists.wisc.edu for more information.
|09:00||Automating tasks with the Unix shell|
|13:00||Building programs with Python|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.
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).
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, try
typing the escape 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. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
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.
Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we highly recommend Anaconda, an all-in-one installer with many of the most-often-used packages.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine). NOTE: if you already have installed Python version 2.x using the Anaconda installer, you need not download another installer for version 3.x. You can set up a virtual installation of Python version 3, switch between your Python versions, and remove the version 3 installation at any time. Ask your instructors how to do this using the conda package manager that you already have installed.
We will teach Python using the Jupyter (formerly IPython) notebook, an interactive programming environment that uses your 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.
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).