Nov 28-29 2018, 9:00am - 6:00pm
Nov 30 2018, 9:00am - 1:30pm
Instructors: Iñigo Aldazabal, Francisco J. Martínez-Murcia, Bryan Zaldivar, Alfonso Nuñez
Helpers: E. Ambite, E. de Córdoba, A. Díaz-Gil, D. Gordo, M. Ramírez
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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, post-doctoral researchers and other researchers You don't need to have any previous knowledge of the tools that will be presented at the workshop.
When: Nov 28-29 2018, 9:00am - 6:00pm. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (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.
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 (using contact details below) and we will attempt to provide them.
Contact: Please email email@example.com for more information.
Please be sure to complete these surveys before and after the workshop.
|09:20||Software setup and account signup|
|09:45||Introduction to the Unix shell|
|11:30||Introduction to the Unix shell (continued)|
|14:30||Version control with Git|
|16:30||Version control with Git (continued)|
|09:20||Doors opening, setup, personal doubts, ...|
|09:25||Review of day 1|
|09:30||Programming in Python|
|11:30||Programing in Python (continued)|
|14:30||Introduction to Machine Learning|
|16:30||Introduction to Machine Learning (continued)|
|09:20||Doors opening, setup, personal doubts, ...|
|09:25||Review of day 2|
|09:30||HPC in half-a-day|
|11:30||HPC in half-a-day (continued)|
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. Choose your OS below for detailed installation instructions
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 a remote repository. 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 IFT's GitLab for parts of the Git lesson. We encourage you to create a GitiLab account if you don't have one already.
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. It should be proposed as an option in the Git Bash installation. Please follow the installation procedure of Git Bash and select nano when asked.
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research 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 Anaconda3-and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
cd DownloadsThen, try again.
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).