Sep 19-21, 2016
13:00-18:00 Day 1, 09:00-18:00 Day 2, 09:00-17:00 Day 3
Instructors: Toby Hodges, Luis Pedro Coelho, Malvika Sharan, Thomas Schwarzl, Mike Smith, Frank Thommen, Georg Zeller
Helpers: Grant Adey, Natalie Romanov, Renato Alves, Marc Gouw
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: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will know a little bit of command line/programmatic computer usage, but not consider themselves an expert. The target student will have written a for loop in some language before, but will not know what Git is (or at least not be very comfortable with advanced Git usage).
Registration: You must be registered in order to attend the course. Registration for the workshop is available through the EMBL Course & Conference Office. There you will also find details of the venue, travel/directions and accommodation in Heidelberg.
Requirements: Participants are required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.
Contact: Please mail toby[dot]hodges[at]embl[dot]de for more information.
Please be sure to complete these surveys before and after the workshop.
|13:00||Introduction & Ice Breaker|
|13:30||Automating tasks with the Unix shell|
|16:30||Introduction to Python Scripting I|
|09:00||Introduction to Python Scripting II|
|13:00||Version Control with Git and GitHub|
|09:00||Scientific Python and Working with Biological Data|
|10:45||Pipeline Management with SnakeMake I|
|13:00||Pipeline Management with SnakeMake II|
|14:45||HPC Cluster Job Submission|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Participants are encouraged to bring their own laptop to work on, if they have access to one, but pre-installed systems will be available for everyone to use in the teaching lab. If you can bring your own laptop, please make sure that you have the following installed.
(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.
cmdand press [Enter])
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen pressing [Enter]
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
See the Git installation video tutorial
for an example on how to open the Terminal.
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).
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
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. See the Git installation video tutorial for an example on how to open nano. 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 strongly 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 Anaconda3-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).