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We are going to be using the following major software for the class:

For the class and homework we will use:



It’s common to run into problems with installation - don’t worry, we’re expecting that. One of the things we are teaching in this class is how to solve problems like installing and using scientific software. So, if you run into trouble - great - that will be a good opportunity for us to work together on a not-trivial problem.

If you are on Windows, please come see us, you will probably have a harder time getting your install working.

For later classes you will also need one of:

  • MATLAB installed on your laptop or;
  • an account on the neuro cluster (so you can run MATLAB / SPM remotely).

Talk to your instructors if you need help with either of these options.

Installation check

Check your installation is correct by downloading this check_install.py script, and running it from the terminal with:

python3 check_install.py

You should see this printed to your terminal:

Congratulations, all checks passed

If you see anything else, copy and paste what you see into an email, and send it to one of your Instructors.

Why Python 3?

“Why Python 3?” is really two questions – “why Python?” and “why Python version 3”.

Python is well-suited to scientific computing for many reasons.

Python code is famously easy to read, and Python has become a common choice for introductions to programming – see for example the Berkeley CS61A course and the MIT introduction to computer science and programming.

The CS61A course notes have a good introduction to the benefits of Python. You may want to read 10 reasons Python rocks for research for a comparison between Python and MATLAB.

Berkeley teaches its new data science courses using Python.

The current version of Python at the time of writing was version 3.5. Python versions 3.0 and greater (such as 3.5) differ in significant ways from earlier versions, such as version 2.7. Many people still use Python 2.7, but because the versions are not fully compatible, we have standardized on Python 3.

For the class, you will need a version of Python >= 3.4.

Why Atom?

We’re going to press you pretty hard to use the Atom text editor.

Choosing an editor is a personal decision, and one we recommend you invest some time in. For example, your instructors, outside the class, usually use vim.

But, for the class, we will be using Atom, and we strongly suggest you do the same. This is for several reasons. Atom:

  • is a high-quality open-source text editor with installers for Windows, OSX and Linux;
  • doesn’t need a lot of configuration to get started;
  • can be configured to work in a very similar to way to other text editors you may be used to, such as vim (vim-mode; ex-mode) and emacs (emacs-mode);
  • can be used to run code interactively, with the hydrogen plugin;
  • has git integration built-in.