These simulations are to reproduce the findings from Ziegler, L., Zenke, F., Kastner, D.B. and Gerstner, W. (2015). Synaptic consolidation: from synapses to behavioral modeling. JNeurosci 35.3 http://www.jneurosci.org/content/35/3/1319.full
ZynapseConnection
Implements the excitatory connection object for complex
synaptic plasticity with protein-dependent consolidation.
ZynapseMonitor
Monitors the plasticity-related proteins (PRP) level
as well as the mean and standard deviation of g(t)
(the synapse specific tag-gating trace).
PRPGroup
Implements an Adaptive Integrate and Fire neuron group
with PRPs.
To run slice experiment simulation as described in Figure 3A of Ziegler et al. (2015), you need to install and compile Auryn v0.8.0-dev (most likely it will work with more recent commits of the develop branch of Auryn too). In the following we will assume that you have git installed and up and running on your system. Moreover, you have all dependencies to compile Auryn installed.
In essence do the following:
$ cd ~
$ git clone https://github.com/fzenke/auryn.git
$ cd auryn
$ git checkout -b version0.8 v0.8.0-beta3
$ cd build/release
$ make
Should you have difficulties compiling the simulator please refer to the
installation and troubleshooting section in the manual (www.fzenke.net/auryn).
If you had auryn already installed and have problems checking out version 0.8
run git fetch --tags
.
Now go to the installation directory of the src/
simulation code (when you are
reading this, chances are you are already in this directory). And run make
there (if you cloned the repository in some other place than ~
, edit the first line of
the Makefile accordingly). This should build the necessary Auryn libraries that implement
plasticity and the simulation libraries. For instance the simulation program sim_frey
is the
one behind Figure 3A in Ziegler et al. (2015).
Invoking $ ./sim_frey
, or $ mpirun -n 2 sim_frey
for example,
will generate an input raster and run the simulation of a weak tetanus (WTET) with a total
time of one hour. For other options run a simulation with the flag -h
or --help
.
Assuming you have gnuplot installed on your system, go to the directory where you saved the results
(editable with the flag --dir
in sim_frey) and run this line in gnuplot
plot "frey_wtet_x.1.wgs" w l t 'weight', "frey_wtet_y.1.wgs" w l t 'tag', "frey_wtet_z.1.wgs" w l t 'scaffold'
(this is if you ran the simulation on two nodes, else change .1
accordingly).