Nov 6-7, 2014
9:00 am - 5:00 pm
Instructors: Laurent Gatto, Robert Stojnic
Helpers: Frank Pennekamp, Peter Fields, Jelena Aleksic
Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on workshop will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Who: This boot camp is an example-driven two-day workshop on advanced R skills. Short tutorials alternate with hands-on practical exercises, and participants are encouraged both to help one another, and to try applying what they have learned to their own research problems during and between sessions. Participants should bring their own laptops to work on.
Contact: Please mail email@example.com for more information.
The aim of the workshop is to provide a set of tools to enable a more structured, efficient and systematic use of programming in computational sciences. We will address the following points throughout the course:
Some of these topics will be addressed through the development of an R package that applied object oriented programming. The main thread that we will use is the definition and manipulations of generic and biological sequences that will, eventually, materialise into a fully fledged package.
See the course repo for a detailed programme, relevant content and the course material.
To participate in a Software Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your workshop.
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.
Git is a state-of-the-art version control system. It 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.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection
After installing Python and Git Bash:
nano is the editor installed by the Software Carpentry Installer,
it is a basic editor integrated into the lesson material.
Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.
For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager, e.g. for Debian/Ubuntu
apt-get install r-base or
yum install R.
Also, please install the