tom83b / matsim

Package primarily for simulation of the MAT model

MATSim

MATSim is a package for simulation of the MAT (Multi-timescale Adaptive Threshold) model (Kobayashi et al., 2009), i.e., a non-resetting leaky membrane equipped with a dynamic firing threshold.

Two following modes of membrane stimulation are possible:

• Conductances (with reversal potentials) modelled as Poisson shot noise with an exponential envelope
• Conductances (with reversal potentials) modelled as an Ohrstein-Uhlenbeck process

The package is written in C++ and wrapped with Cython for high efficiency.

Installation

Dependencies

MATSim requires:

• Python (>= 3.6)
• NumPy (>= 1.16.3)
• Pandas (>= 0.24.2)

Although older versions might be sufficient, they haven't been tested.

User installation

Using pip

Install the package using pip:

pip install matsim

Compilation from source

First, use Cython to create the file matsim.cpp (in the directory matsim):

cython --cplus matsim.pyx

Then use the setup file to install the package:

python setup.py install