Below you find installation instructions for all the software used in our tutorials. There are two ways you can go about this:

• Install Virtualbox and download a VM from the relevant tutorial. This VM will have all the necessary software preinstalled.
• Install the software yourself (which won't be trivial depending on the OS you are using): Neuron, IPython notebooks, eFEL, BluePyOpt

Please test your installation well before the tutorial starts.

Foremost, if you have any questions/problems regarding installing this software on your system, please let us know on our chat channel.

We provide Virtual Machines with preinstalled software. To run these VMs it is necessary to install the VirtualBox. Linux, MacOS and Windows are supported.

You can download the necessary installers from their download page, and the follow installation instructions they provide. It should be sufficient to only install the 'VirtualBox platform packages'.

To test your installation download the VM relevant to your Tutorial, and boot it in VirtualBox. An example of such a VM (used for the HBP School 2016 tutorial) is located here.

Make sure you can access external website inside the VM. To test this, open a browser, and go to https://bbp.epfl.ch/nmc-portal/welcome

An alternative is to install all the required software packages manually on your desktop. We want to warn you that this might not be trivial.

A requirement for the installation of all the tools below is Python. We need version 2.7+ (some tools are not compatible with Python 3 yet).

Linux distributions should come with Python preinstalled. It could be that Python 2 is not automatically installed. In the latest Ubuntu e.g. you might have to install it using:

sudo apt-get install python2.7

Recent MacOS versions come with Python out of the box.

Installation instructions are here.

Once you have Python installed, you should make sure pip is installed correctly. And you should also work inside a Python virtualenv, see instructions here

Open a commandline utility, and type

python -c 'import os; print os.getcwd()'

which should print out the name of the directory you are currently in.

<<<<<<< HEAD

For the Neuron simulator installation instructions, see here.

======= This

pip install pip --upgrade

should install the latest version of pip.

Also make sure you managed to set up and activate a Python virtualenv.

For all functionality work you need to have Neuron installed with Python and X11 support, and you need to be able to compile MOD files. Instructions for different operating systems are provided here

Open a commandline utility, and type

python -c 'import neuron; soma = neuron.h.Section(); print soma.v'

which should print out the Neuron banner, and the value '-65'.

When you type

nrngui

the Neuron graphical user interface should pop up.

You should be able to compile Neuron MOD using the command:

nrnivmodl

It's best to test your entire installation by running and downloading one the NMC portal models, as described in the 'Running NEURON model packages' section of https://bbp.epfl.ch/nmc-portal/tools (the models should be able to be run using both Python and the GUI)

Information is available here

Installing using

pip install jupyter

When you run

jupyter notebook

it should open your browser on a page connected to the jupyter notebook kernel.

You can install BluePyOpt using

pip install bluepyopt

this should also automatically install eFEL as a dependency.

Running

python -c 'import efel; print efel.getFeatureNames()'

should print a list of all the eFeature names

Running

 python -c 'import bluepyopt; print bluepyopt.__version__'

should print the BluePyOpt version installed