May 25, 2017
10:00AM-12:00PM
Instructors: Joslynn Lee, Arron Shiffer
Helpers: Agnes Chan, Anne Sylvester, Dave Jackson
Adapted from Software Carpentry workshops, SWC 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, skills and tools, for working more effectively with data. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. This is a very short form from the traditional 2-day workshop.
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.
Why: This is presented as part of the 2017 Genomic Science Leadership Initiative Workshop. As part of the professional development sessions for students and faculty but mostly to prepare skills for microbiome analysis.
Who: The course is aimed at students and researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop. You can always come back to do this in your free time.
Where: Fort Lewis College, 1000 Rim Drive, Durango, CO 81301. Get directions with OpenStreetMap or Google Maps.
When: May 25, 2017. Add to your Google Calendar.
Requirements: This workshop, we work in a computer lab. But in the future, participants must use their own 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.
Contact: Please email joslynnlee@gmail.com for more information.
| 10:00 | CyVerse Overview + Atmosphere Setup |
| 10:15-10:45 | How to read a journal article |
| 10:45-11:00 | Break |
| 11:00-12:00 | The Unix Shell |
| 11:00 | Introducing the Shell |
| 11:20 | Navigating Files and Directories |
| 11:30 | Break for freestyle python |
| On your own | Working with Files and Directories |
| On your own | Pipes and Filters |
| On your own | Loops |
| On your own | Shell Scripts |
| On your own | Finding Things |
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 Mac OS X 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.
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.
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.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).
We will teach Python using the IPython 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).