Setup

The short version

To get the most out of Neurohackademy, we recommend that you arrive at the course with the following software already installed:

  • A command-line shell (we recommend Bash)
  • The version control system Git
  • A text editor you’re comfortable with (nano, emacs, vi, Sublime Text, Atom, VSCode, etc.)
  • Python 3 (not Python 2!)
  • R
  • A modern browser (e.g., a recent build of Chrome, Safari, Edge, etc.)

If you already have all of the above software tools/packages  installed, or are confident you’ll be able to install them by the time the course starts, you can probably stop reading here. The rest of this page provides more detail on installation procedures for each of the above elements, with separate instructions for each of the three major operating systems (Windows, OS X, and Linux).

Detailed installation instructions

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial

    1. Download the Git for Windows installer.
    2. Run the installer and follow the steps bellow:
        1. Click on “Next”.

        1. Click on “Next”.


        1. Keep “Use Git from the Windows Command Prompt” selected and click on “Next”.

          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.

        1. Click on “Next”.


        1. Keep “Checkout Windows-style, commit Unix-style line endings” selected and click on “Next”.


        1. Keep “Use Windows’ default console window” selected and click on “Next”.

        1. Click on “Install”.


        1. Click on “Finish”.
    3. If your “HOME” environment variable is not set (or you don’t know what this is):
        1. Open command prompt (Open Start Menu then type cmd and press [Enter])
        2. Type the following line into the command prompt window exactly as shown:setx HOME "%USERPROFILE%"
        3. Press [Enter], you should see SUCCESS: Specified value was saved.
        4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities).
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.

Linux

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
install anything.

Git

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 on GitHub. 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.

Windows

Git should be installed on your computer as part of your Bash
install (described above).

Mac OS X

Video Tutorial

For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent “mavericks” installer from
this list.
After installing Git, there will not be anything in your /Applications folder,
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”
available here.

Linux

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.

Text Editor

There are dozens of popular text editors out there, and we take no stance on which you should use. We do, however, strongly suggest using a highly customizable editor that’s optimized for writing code (e.g., with features like automatic syntax highlighting for different languages, code completion, etc.). Good choices available on all major OSs include VSCode, Sublime Text, Atom, or nano. Power users may be more comfortable with emacs or vim (though note that vim—which is the default text editor on Mac OS X and Linux—is not famous for being intuitive). Below we provide installation instructions for nano, which is a very basic editor you can use directly from the shell. But we probably recommend using one of the other editors mentioned above (most of which have one-click installers available on all platforms).

Windows

Video Tutorial

nano is a basic editor. To install it, download the Windows installer
and double click on the file to run it.
This installer requires an active internet connection. Be aware that you must add its installation directory to your system path.
Please ask your instructor to help you do this.

Mac OS X

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.

Linux

nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.

Python

Python is a popular language for research computing, and great for general-purpose programming aswell. 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., 3.7 is fine).

We will often use the IPython (Jupyter) 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).

Windows

Video Tutorial

    1. Open https://www.anaconda.com/distribution/ with your web browser.
    2. Download the Python 3 installer for Windows.
    3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial

    1. Open https://www.anaconda.com/distribution/ with your web browser.
    2. Download the Python 3 installer for OS X.
    3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open https://www.anaconda.com/distribution/ with your web browser.
  2. Download the Python 3 installer for Linux.
    (Installation requires using the shell. If you aren’t
    comfortable doing the installation yourself
    stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type 
    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 Downloads

    Then, try again.

  5. Press enter. You will follow the text-only prompts. To move through
    the text, press the space key. Type yes and
    press enter to approve the license. Press enter to approve the
    default location for the files. Type yes and
    press enter to prepend Anaconda to your PATH
    (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Video Tutorial

Install R by downloading and running
this .exe file
from CRAN.
Also, please install the
RStudio IDE.
Note that if you have separate user and admin accounts, you should run the
installers as administrator (right-click on .exe file and select “Run as
administrator” instead of double-clicking). Otherwise problems may occur later,
for example when installing R packages.

Mac OS X

Video Tutorial

Install R by downloading and running
this .pkg file
from CRAN.
Also, please install the
RStudio IDE.

Linux

You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo yum install R). Also, please install the
RStudio IDE.

Docker

Docker is a system for creating and running small, isolated virtual machines (“containers”). We often use docker to install software together with its dependencies.

Windows

There are a few things to consider, before starting the installation. Please read about them here. The most important thing to note is that if you have 64bit Windows 10 Pro, Enterprise and/or Education, run Docker for windows, Otherwise install docker toolbox.
Instructions for the installation itself are here .

Mac OS X

There are a few things to consider, before starting the installation. Please read about them here. The instructions for installation are here.

Linux

Instructions for different flavors of linux are avalible at the following links:

  1. Ubuntu: https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/
  2. Debian: https://docs.docker.com/engine/installation/linux/docker-ce/debian/
  3. Centos: https://docs.docker.com/engine/installation/linux/docker-ce/centos/
  4. Fedora: https://docs.docker.com/engine/installation/linux/docker-ce/fedora/