Software Carpentry: QUT - Research Bazaar (R)

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 and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. We are running two Software Carpentry workshops in parallel as part of the "Research Bazaar" in Brisbane. This workshop will cover task automation with the Unix shell Bash, programming with R and version control with Git. (The other workshop is the same, except it will cover Python instead of R.)

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: All Research Bazaar attendees are welcome to attend this course. We particularly encourage early career researchers to attend and kickstart their digital skills. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room P505, P Block, Queensland University of Technology, Gardens Point Campus. Get directions with OpenStreetMap or Google Maps.

Requirements: You will need to bring a laptop with the specific software packages installed as detailed below. You are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail s.hames@uq.edu.au for more information.

Schedule

Day 1

08:30	Setting up and software installation help
09:00	Automating tasks with the Unix shell
10:30	Morning tea
11:00	Automating tasks with the Unix shell
12:30	Lunch break
13:30	Introduction to R
15:00	Afternoon tea
15:30	Rstudio, R help
16:45	Wrap-up

Day 2

08:30	Setting up and software installation help
09:00	Graphing and using packages in R
10:30	Morning tea
11:00	Making your own R scripts
12:30	Lunch break
13:30	Version control with Git - Intro
15:00	Afternoon tea
15:30	Version control with Git - Collaboration
16:45	Wrap-up

Etherpad: http://pad.software-carpentry.org/ResBaz-BNE-R.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

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

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...

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...

Wireless Internet Access

You will be able to access wireless internet through eduroam - check your institutions IT support pages for how to connect. If you aren't affiliated with an eduroam institution we will have temporary usernames and passwords for you on the day.

Setup Option 1: Local Installation On Your Laptop

As an alternative to the DIT4C cloud option, you can install the software locally on your machine, using the instructions below. Please arrive before 9:00am to get your install checked by a helper. We can also help you setup your own machine during the ResBaz Hacky Hour on the day after the workshop.

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 and follow the steps bellow:
1. Click on "Next".
2. Click on "Next".
3. Click on "Next".
4. Click on "Next".
5. Click on "Next".
6. Select "Use Git from the Windows Command Prompt" and click on "Next". 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.
7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
8. Select "Use Windows' default console window" and click on "Next".
9. Click on "Next".
10. Click on "Finish".

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.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

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 the RStudio IDE.

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.

Setup Option 2: The DIT4C cloud

We have a cloud based environment available with all the software needed for the workshop pre installed. For this option to work you will need to setup Eduroam (differs for each institution) so you have a working wireless internet connection.

We'll give instructions on how to connect to this on the day of the workshop.