14-15 Dec, 2015
9:30 am - 5:30 pm
Instructors: Aleksandra Pawlik, Aleksandra Nenadic
Helpers: Clair Barrass, Simone Di Cola, Suzanne M. Embury, Toni Collis, Mireya Paredes
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.
Who: The course is aimed at female postgraduate students, researchers and engineers who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Contact: Please mail admin-uk@software-carpentry for more information.
Women in HPC aims to increase participation of women in the HPC community by providing people with the opportunities to find out about HPC technology and the benefits it can have on their work. We provide events to bring together female HPC scientists, researchers, developers, users, system administrators and technicians as well as showcasing the work of inspiring role models. By providing courses designed for and led by women we hope to reduce the barrier to participation of women in the HPC community.
The Software Sustainability Institute's mission is to cultivate better, more sustainable, research software to enable world-class research ( better software, better research). Software is fundamental to research: seven out of ten UK researchers report that their work would be impossible without it.
ARCHER, the UK's national supercomputing service, offers training in software development and high-performance computing to scientists and researchers across the UK. As part of our training service we are running a two-day Data Carpentry workshop.
ELIXIR-UK, a part of the ELIXIR project community, is taking a UK and European lead in training, as well as co-leading the ELIXIR platform for integration and interoperability of data and services. in order to facilitate access to data infrastructure and training for scientists in both academia and industry.
|09:30||Welcome and setup|
|10:00||Automating tasks with the Unix shell part 1 Materials|
|11:30||Automating tasks with the Unix shell part 2|
|13:30||Structured programming with Python part 1 Materials|
|15:30||Structured programming with Python part 2|
|18:00||Hot buffet and drinks|
|09:30||Python functions and modules|
|11:30||Version control with Git part 1 Materials|
|13:30||Version control with Git part 2|
|15:30||Quality assurance in Python|
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.
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.
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.
Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific 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 Anaconda-and then press tab. The name of the file you just downloaded should appear.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).
Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.