The data and scripts necessary to reproduce the results (Figs. 7-12) are all contained in the compressed file "data-sim-PlosCB.tar.gz". The code should run as-is under any Linux distribution, provided that the necessary open-source software is installed. All software should be available also for MacOS (not tested).

Most software is also available for Windows. However, a replacement for the plotting software XmGrace is needed, as well as some editing to the scrips because of path handling.

For assistance please contact: davide.bernardi (at) bccn-berlin.de

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SOFTWARE REQUIREMENTS:

1) C++ code:

• C++ compiler
• boost (www.boost.org)
• GNU scientific library (fftwwww.gnu.org/software/gsl)
• fftw3 (www.fftw.org)
• OpenMP (www.openmp.org)
• cmake (www.cmake.org)

2) Python 2.7 + numpy/scipy. Using Anaconda is recommended to create a python 2 compatible environment (www.anaconda.com)

3) HTCondor queuing system to manage the large number of simulation trials (https://research.cs.wisc.edu/htcondor/index.html)

4) Plotting software xmgrace (https://plasma-gate.weizmann.ac.il/Grace)

INSTRUCTIONS: 1) After installing all required software packages, unzip "data-sim-PlosCB.tar.gz" and open a terminal in the "build" subdirectory.

2) Prepare the Makefile by using cmake: cmake ../network_source_code -DCMAKE_BUILD_TYPE=Release

3) Build the C++ executable by typing make

4) To run all simulations and make all plots, move back to the main directory and call the main script ./main_script.py

5)./main_script --help for more options

NOTES:

• With the default number of trials used in the paper (10000) simulations require about two weeks on ~200 computing cores. The number of trials can be changed with the optional argument --trials. Due to the weak effect size, at least a few thousand trials are necessary to obtain a meaningful picture.
• Child scripts can be run separately to produce single figures.
• Standard network parameters are stored in "./parameter_sets/standard.parameters". It is possible to save a different parameter combination with the .parameters extension (e.g. myparameters.parameters) and run the network simulations with these parameters by calling the main script with the --parameter option:

./main_script.py --par ./parameter_sets/myparameters.parameters