Auryn classes and simulation to reproduce slice experiments on synaptic consolidation.
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.
Running an example
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-beta3. 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.
Download and compile Auryn
In essence do the following:
$ cd ~ $ git clone https://github.com/fzenke/auryn.git $ cd auryn $ git checkout -b v0.8.0-beta3 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 0.8.0 beta3
git fetch --tags.
Compile simulation classes and programs
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
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).
$ ./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
Plot the result
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