Jul 2-3, 2015
10:00 am - 4:30 pm
Instructors: Kirill Tsyganov, Steve Androulakis, Roxane Legaie, Paul Harrison
Helpers: Jerico Revote, Stuart Archer, Andrew Pattison, Adele Barugahare, David Powell, Haroon Naeem, Simon Michnowicz, Grischa Meyer, Jason Rigby
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
This hands-on workshop will cover an introduction to the command line (Unix shell), version control (Git and Github) and R (programming language and software environment for statistical computing and graphics).
Towards the end of the workshop, we will be applying our newly aquired skills to a bioinformatics (next-gen sequencing data) example.
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.
Contact: Please mail email@example.com for more information.
|10:00||Registration and Welcome|
|10:30||Getting started with the Unix shell|
|13:00||Getting started with the Unix shell|
|15:00||Git and GitHub|
|10:00||Programming with R|
|13:00||Programming with R|
|15:00||Bioinformatics with R|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
This method requires far less work. Only install the tools below as a backup, or if you'd like the tools on your own computer for your own work later on.
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. Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly. 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.
Install Git for Windows by downloading and running the installer. 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
/Applications/Utilities). 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
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).
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
After installing Git, there will not be anything in your
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"
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.
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.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.