Software Carpentry: iPlant Collaborative, University of Arizona

General Information

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 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, postdocs, faculty, and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Manuel Pacheco Integrated Learning Center Rooms 119 and 141, 1500 E University Blvd, Tucson, AZ 85719. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct. Additionally, participants will need to have a GitHub account and an iPlant account for this workshop. To get a free GitHub account, participants can go to github.com and click the Sign Up button. For an iPlant account, participants can set up an account at the User Portal. NOTE: please use your institutional email for the signup (e.g. your email.arizona.edu address) or things may not work.

Setup help: Setup help for any of the required software, GitHub accounts, or iPlant accounts will be available at Bio5 on the Wednesday, Thursday, and Friday before the workshop. Please email Blake Joyce to arrange for assistance or to answer any setup questions you may have.

Contact: Please mail hilgert@email.arizona.edu for more information.

Room 137 Etherpad

Room 141 Etherpad.

Schedule

Saturday

09:00	Scripting your analyses with R
10:30	Coffee
12:00	Lunch break
13:00	Automating analyses with the shell
14:30	Coffee
16:00	Wrap-up

Sunday

09:00	Version control with Git
10:30	Coffee
12:00	Lunch break
13:00	Bringing it all together: versioned, scripted research in the cloud
14:30	Coffee
16:00	Wrap-up

For your reference, here is a link to the R gapminder Software Carpentry lessons.

Syllabus

Programming in R

Working with vectors and data frames
Reading and plotting data
Creating and using functions
Loops and conditionals
Using R from the command line
Reference...

The Unix Shell

Files and directories
History and tab completion
Pipes and redirection
Looping over files
Creating and running shell scripts
Finding things
Reference...

Version Control with Git

Creating a repository
Recording changes to files: add, commit, ...
Viewing changes: status, diff, ...
Ignoring files
Working on the web: clone, pull, push, ...
Resolving conflicts
Open licenses
Where to host work, and why
Reference...

Setup

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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. 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. This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

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). You may want to keep Terminal in your dock for this workshop.

Linux

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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

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.

Linux

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.

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 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.

Windows

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 read through the suggestions here if you'd like to try and do this on your own, and/or ask your instructor to help you do this.

Mac OS X

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 Text Wrangler or Sublime Text.

Linux

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.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Install R by downloading and running this .exe file from CRAN. Also, please install RStudio.

Mac OS X

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

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 yum install R). Also, please install the RStudio IDE.