August 13-14, 2018
9:00 am - 4:30 pm
Instructors: Jingchao Zhang, Adam Caprez, Carrie Brown
Helpers: John Thiltges, Eric Zhang, Huijun Zhu, Caughlin Bohn, Mitchell Clark
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:
| University of Nebraska-Lincoln | University of Nebraska at Omaha |
|---|---|
| Scott Engineering Center - Room 111 844 N 16th St Lincoln, NE 68508 Get directions with OpenStreetMap or Google Maps. |
Peter Kiewit Institute - Room 164 1110 S 67th St Omaha, NE 68182 Get directions with OpenStreetMap or Google Maps. |
No seats left at this location |
When: August 13-14, 2018. Add to your Google Calendar.
Cost: $25 for NU affiliates / $50 for non-NU affiliates
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.
Parking:
| University of Nebraska-Lincoln | University of Nebraska at Omaha |
|---|---|
| Parking is available in the lot across the street from the Scott Engineering Center at the corner of 16th and W. Attendees from other NU campuses can park in this lot using the pass from their home institution. Student passes are eligible to park in the spots designated as "C" areas and Staff/Faculty passes can be used in the "A" areas. Metered parking is also available. Additional information on the parking policy can be found on the Parking and Transit Services website. |
Parking is available in the lots adjacent to the Peter Kiewit Insitute. Attendees with UNMC passes can park either in the student lot to the northwest of the building or in the Pacific Street garage located across 67th street once they register their passes with UNO Parking Services. Please contact Parking Services to register your pass prior to attending. Daily visitor passes are also available to purchase at the kiosk in the Pacific Street garage. Additional information on the parking policy can be found on the UNO Parking Services website |
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
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.
Contact: Please email hcc-support@unl.edu for more information.
Please be sure to complete these surveys before and after the workshop.
| Before | Pre-workshop survey |
| 08:30-09:00 | Set-up |
| 09:00-10:30 | Automating tasks with the Unix Shell |
| 10:30-10:45 | Coffee break |
| 10:45-12:00 | Automating tasks with the Unix Shell (continued) |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Automating tasks with the Unix Shell (continued) |
| 14:00-14:30 | Version Control with Git |
| 14:30-14:45 | Coffee break |
| 14:45-16:30 | Version Control with Git (continued) |
| 16:30 | Wrap-up |
| 08:30-09:00 | Set-up |
| 09:00-10:30 | Programming in Python |
| 10:30-10:45 | Coffee break |
| 10:45-12:00 | Programming in Python (continued) |
| 12:00-13:00 | Lunch break |
| 13:00-14:30 | Programming in Python (continued) |
| 14:30-14:45 | Coffee break |
| 14:45-16:30 | Programming in Python (continued) |
| 16:30 | Wrap-up |
| 16:30 | Post-workshop Survey |
| 16:40 | END |
add, commit, ...status, diff, ...clone, pull, push, ...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.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.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 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
this list.
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.
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, 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.
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.
Others editors that you can use are Text Wrangler or Sublime Text.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Others editors that you can use are Gedit, Kate or Sublime Text.
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.
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.
yes and
press enter to approve the license. Press enter to approve the
default location for the files. Type yes and
press enter to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).