Installation

Using docker (recommended)

We recommend using our docker container which has all the dependencies pre-installed.

You can run the docker image with:

docker run mirok/neuronmi

Manual installation

The following are dependencies of neuronmi and how they can be obtained.

IMPORTANT: the current version runs on Python 2.7. We are currently working on a Python 3 update.

1. Generating meshes for neuron simulations with EMI models We rely on Gmsh for both mesh generation and geometry definition. All is done via the python API of Gmsh. The gmsh module has to be on python path. For the current shell session this can be accomplished by running

export PYTHONPATH=`pwd`:"$PYTHONPATH"

in the directory where gmsh.py resides (e.g. /usr/local/lib/).

2. Partial differential equation part of EMI The solver requires FEniCS version 2017.2.0. In our experience the simplest way of installation that also plays along nicely with Gmsh is by using the dedicated Ubuntu package.

3. Ordinary differential equation part of EMI Membrane physics is solved for using cbc.beat (which depends on dolfin-adjoint).

Testing

Run from current directory

python -m unittest discover ./test/mesh;
python -m unittest discover ./test/simulators/solver;