Resources for Students

Software installation instructions

Python

Installation instructions for Python 2.7

We recommend to use the anaconda Python distribution and instructions on how to download and install anaconda on your computer are given here: https://www.continuum.io/downloads.

For Windows and MAC users, after the download, open the file and follow the indicated steps. For Linux users, open a terminal in the folder containing the downloaded file and type:

bash Anaconda2-5.0.1-Linux-x86.sh
for 32 bits version

or

bash Anaconda2-5.0.0-Linux-ppc64le.sh
for 64 bits version

Note that the name of the file will vary depending on the version you downloaded.

Those who run Linux should be aware that installing anaconda may change some package dependencies and cause errors in program executions. An alternative to install Python 2.7 for Linux users with an Ubuntu or Ubuntu-based distribution is to use pip. To do so, type on the terminal:

sudo apt-get update
sudo apt-get install python2.7

Then, install pip by typing:
sudo apt-get install python-pip

To upgrade pip to the latest version:
pip install –upgrade pip

Installation of packages using pip can be done with the following command:
pip install –user PYTHON_PACKAGE_NAME
E.g. if you want to install the numpy package type: pip install numpy.

NEURON

Installation instructions for NEURON

Install NEURON 7.5 from http://www.neuron.yale.edu/neuron/download
Please choose the correct installer for your system (64 bit if you have a 64 bit
computer and operating system) and follow the instructions for your system.

For Mac and Windows users we recommend that you install NEURON 7.5 on your
computer following the step-by-step instructions in the pdf files:
For Mac users: http://neuron.yale.edu/ftp/neuron/nrn_mac_install.pdf
For Windows users: http://neuron.yale.edu/ftp/neuron/nrn_mswin_install.pdf

On a Mac, after you have installed NEURON 7.5 as described in the above pdf file it should be installed in /Applications/NEURON-7.5

You can then add /Applications/NEURON-7.5/nrn/x86_64/bin to your PATH environment variable in .bash_profile in your home directory. This will allow you to run the commands nrnivmodl and nrngui from the command line in a terminal, like under Linux.

To test whether you have correctly installed NEURON, download and run the following example https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=2488
On a Terminal, go to the patdemo directory where you unpacked the example. Type:
nrnivmodl
nrngui demofig1.hoc

You have correctly installed NEURON if you can see a window showing action potentials after you choose one of the four cell types and click Init & Run in the RunControl window.

neuroConstruct

To install the latest version of neuroConstruct on your laptops, please follow the instructions given at http://www.neuroconstruct.org/docs/install.html

XPP

To install XPP on your laptops, please follow the instructions given at http://www.math.pitt.edu/~bard/xpp/xpp.html

NEST

To install the latest version of NEST (2.14) on your laptops, please follow the instructions given at: http://www.nest-simulator.org/installation/.

Note that NEST runs under Linux distributions and Mac OS but not under Windows. To run NEST under Windows you will need a virtual machine, e.g. VirtualBox (http://www.virtualbox.org/), installed.

Requirements and instructions for installing NEST from source code:

– Dependencies:

To build NEST, you need recent versions of CMake and libtool; the latter should be available for most systems and is probably already installed.
If you are using apt package manager, type on a terminal:

sudo apt-get install CMake
sudo apt-get install libtool

– Standard configuration

To install the packages required for the standard configuration use the following command line:

sudo apt-get install -y build-essential cmake libltdl7-dev libreadline6-dev libncurses5-dev libgsl0-dev python-all-dev python-numpy python-scipy python-matplotlib ipython openmpi-bin libopenmpi-dev python-nose

– Basic steps to compile and install NEST from source code:

Download NEST (http://www.nest-simulator.org/download)

Unpack the tarball:

tar -xzvf nest-simulator-x.y.z.tar.gz

Create a build directory:

mkdir nest-simulator-x.y.z-build

Change to the build directory:

cd nest-simulator-x.y.z-build

Configure NEST:

cmake -DCMAKE_INSTALL_PREFIX:PATH=</install/path> </path/to/NEST/src>

with additional cmake options as needed (see INSTALL file: https://github.com/nest/nest-simulator/blob/master/INSTALL; /install/path should be an absolute path)

Compile by running:

make

Install by running:

make install

Run tests by running

make installcheck

See the Getting started pages in the official website to find out how to get going with NEST

http://nest-simulator.org/getting-started/

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