This file is part of https://github.com/fzenke/pub2013ca_inference_net and contains code used to simulate the spiking neural networks in

Lütcke, H., Gerhard, F., Zenke, F., Gerstner, W., and Helmchen, F. (2013). Inference of neuronal network spike dynamics and topology from calcium imaging data. Front Neural Circuits 7. http://journal.frontiersin.org/article/10.3389/fncir.2013.00201/abstract

The code for the first part of the paper to simulate calcium traces and inferring APs using the peeling algorithm can be found in the Github repository of Henry Lütcke: https://github.com/HelmchenLab/CalciumSim

To run the simulation you need a compiled version of the network simulator Auryn, which can be found at http://www.fzenke.net/auryn and http://github.org/fzenke/auryn. Requires Auryn v0.8

Note that the output files are VERY large!

To run the simulation it will suffice on most Linux systems to call 'make' from the command line. This will unpack the time series file with the brownian rate modulation, compile the code and run the simulation. Output files are written to the subdirectory ./data.

The simulation generates the following human readable files:

lgnet.0.e.prate : Firing rate of exc population
lgnet.0.i.ras : Spikes from inh population
lgnet.0.e.ras : Spikes from exc population
lgnet.0.p.ras : Spikes from Poisson population
lgnet.0.e.mem : First couple of seconds of membrane of neuron 123
lgnet.0.log : Logfile
lgnet.0.ee.wmat : Connectivity matrix E->E in MatrixMarket format 
lgnet.0.ei.wmat : Connectivity matrix E->I in MatrixMarket format 
lgnet.0.ie.wmat : Connectivity matrix I->E in MatrixMarket format 
lgnet.0.ii.wmat : Connectivity matrix I->I in MatrixMarket format 

Note that the spikes generated in this step might need further filtering as was done in Lütcke, H., Gerhard, F., et al. (2013)

Enjoy!

-- F. Zenke, Mon Oct 19 23:47:11 PDT 2015