May 25-27, 2016
9:00 am - 4:30 pm
Instructors: Alexandre Manhães Savio, Jean-Christophe Leyder, Oier Echaniz
Helpers: Johan Mårtensson, Olof Strandberg, Peter Mannfolk
Organizers: Johan Mårtensson, Titti Owman
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: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Contact: Please mail firstname.lastname@example.org for more information.
This workshop is possible thanks to the contributions of
Please be sure to complete these surveys before and after the workshop.
|09:00||Software setup and account signup(Oier)|
|09:45||Introduction to the Unix shell (Oier)|
|11:30||Introduction to the Unix shell (continued) (Oier)|
|14:15||Version control with Git (JC)|
|16:00||Version control with Git (continued) (JC)|
|09:00||Set up and review of day 1 (JC?)|
|09:30||Programming in Python (Alex)|
|11:30||Programming in Python (continued) (Alex)|
|14:15||Scientific Python (JC)|
|16:00||Scientific Python (continued) (JC)|
|09:00||Set up and review of day 2(Alex)|
|09:30||Introduction to Nipy (Alex)|
|09:45||Introduction to Nipype (Alex)|
|11:30||Introduction to Nipype (continued) (Alex)|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.
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 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 recommend Python 3 for your projects, however Python 2.7 will also work for this workshop.
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).
Nipype an open-source, community-developed Python initiative under the umbrella of NiPy. It provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.
To run the tutorial you will probably need FSL and SPM correctly installed. You must follow each tools' installation procedure. To check if FSL is correctly installed you can run
fslin a terminal and a window must appear. In order to nipype find SPM you must be able to launch Matlab running
matlabfrom a terminal (tip: include its bin folder in your $PATH) and SPM must be in the Path of Matlab. There is a comprehensive set of instructions to install neuroimaging tools here.
In order to install nipype: If you use Python 2.7 you can install it using
pip install nipype. If you prefer Python 3.4 or 3.5 you will have to install a newer version from the repository, running:
pip install git+https://github.com/nipy/nipype
There are other nipy tools that you may find interesting and you can install using the same scheme as in the previous paragraph.
Please send us an email if you have any question or issue with the setup.
To accelerate the beginning of the course, please have the NiPype repository cloned in your computer. To do this, go to the folder where you want to have the source code folder and run:
git clone https://github.com/nipy/nipype.gitI also need you to download this dataset. And we will start with the notebooks in this repository:
git clone https://github.com/Neurita/nipype-lessons