measim

Simulation of two-dimensional cultured neuronal network

This code implements a neuronal, electrophysiological model by Volman et al, which consists of Morris--Lecar neurons and extended Tsodyks--Markram synapses, on a 2D network to simulate a system of dissociated cultured neurons on a multi-electrode array. Please see the manuscript arXiv:1610.05717 for details of the model and the corresonding experiments. Supplementary files of the manuscript can be found in the pub1 subdirectory of the git repository. Earlier studies employing the code include: arXiv:1402.1959

Prerequite libraries (Debian packages, recommanded verion)

Building from source package: HDF5 (libhdf5-dev, >=1.8.16)
With GUI: glut/freeglut3 (freeglut3-dev, >=2.8.1)

Building from git checkout: autoconf (>=2.69), autoconf-archive (20160916), automake (>=1.15), libtool (>=2.4.6), pkgconf (>=0.9.12)

Build from git

The build system of measim is based on GNU autotools. First check out the source tree and submodules from github:

$ git clone https://github.com/chnchg/measim
$ cd measim
$ git submodule init
$ git submodule update

then build from source with

$ ./bootstrap
$ mkdir build
$ cd build
$ ../configure
$ make

Build from release source package

Download release source package measim-<version>.tar.xz from git and build:

$ tar xf measim-<version>.tar.xz
$ cd measim-<version>
$ mkdir build
$ cd build
$ ../configure
$ make

Executables

After the build process completes successfully, there will be following executables for the simulation:

• rvol: command-line simulation engine use ./rvol --help to see options
• vdmp: dumps mean values of system states as it runs
• vvol: GUI programs for visualized simulation run
• vvlt: Threaded version of vvol to seperate GUI and running codes (unstable, changing parameter while running may lead to crash of the program)