Installation

Installation instructions

ViNERS is a MATLAB-based software package and so you will need to install MATLAB or Octave before installing ViNERS. Note that while Octave is free, ViNERS has not been thoroughly tested on Octave and there will likely be changes which need to be made for Octave-compatibility. When installing MATLAB, be sure to also install the parallel computing toolbox.

I recommend that you also install git, a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

Once you have installed MATLAB and git, simply run install_ViNERS.m. This will walk you through the next steps:

1. Select an installation directory
2. If you have not already done so, git pull ViNERS and unpack in installation directory. If you have downloaded ViNERS from somewhere other than gitlab, I recommend pulling the latest source code.
3. Locate your existing NEURON installation, or download and install NEURON if no installation is found. The button takes you directly to the installer. On unix, NEURON is installed using sudo apt-get install NEURON and some other necessary packages are loaded while we're at it.
4. Locate your existing EIDORS toolbox, or download and install EIDORS if not found.
5. Locate your existing GMSH installation, or download and install GMSH if no installation is found. Note for unix users: the version of GMSH in the apt-get (3.0.6) is out-of-date; ViNERS has been tested to work with GMSH 4.4.1 and 4.8.3 but will not work with version 3.0.6.
6. Unpack ViNERS into a SPARC data structure, roughly based on the BIDS standard, creating /primary, /code, and /source in the installation directory.
7. Compile the neuron ion channel mechanisms. This generates nrnmech.dll with mknrndll (windows) or /x86_64/special with nrnivmodl (unix). On Windows, step-by-step instructions for opening a bash shell, executing cd path/to/ViNERS/source/nrnmech/, and executing mknrndll are provided (mknrndll does not work if called from the MATLAB console).

Manual Installation

If the installer doesn't work for you, you'll need to install ViNERS manually. This is fairly straightforward - you will have to perform steps 2-7 as above. tools.make_SPARC_structure automates most of step 6. At this step, you will need to manually move the contents of the "Source-data" folder into "~/source" and ensure that the downloaded code is correctly placed in the "~/code" folder.

You will also need to manually add the paths for EIDORS, NEURON, and GMSH to the +tools/configuration.json file. IF you delete this file and run tools.configuration('make-new-file') the metadata about your machine should get set up correctly. I recommend doing this after (not before) setting ViNERS into the SPARC structure in case tools.file gives you problems.