## Figures of Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018) A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque cortex.
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This folder contains the scripts to reproduce all figures of Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018) A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque cortex. (under review)
The figure scripts are named according to their ordering in the paper. To execute them, you can choose to either work with newly simulated data or the original data used in the publication.
### Original simulation data
You can retrieve the original data from the Dryad Digital Repository database (TODO: Upload data and insert link). By default, all plot scripts are configured to use the old data (`LOAD_ORIGINAL_DATA = True` in all scripts). You have to download the data and then define the variable `original_data_path` in `config.py`.
### Creating new simulation data
To work with newly simulated data, you first have to run the necessary simulations, by executing `run_simulations.py`. Please note that you will need to provide sufficient resources on an HPC cluster. (TODO: More information)
You then have to set `LOAD_ORIGINAL_DATA = False` in the plot scripts to switch them to using new data.
### Experimental data
Figure 6 requires the experimental data of Chu CCJ, Chien PF, Hung CP. Multi-electrode recordings of ongoing activity
and responses to parametric stimuli in macaque V1, available in the crcns.org database. Please register on [https://www.crcns.org/](https://www.crcns.org/), download the data from [https://portal.nersc.gov/project/crcns/download/pvc-5](https://portal.nersc.gov/project/crcns/download/pvc-5), extract them into a path and then set this path in `helpers.py`.
Figure 8 requires the experimental fMRI data that are contained in this repository in `Fig8_exp_func_conn.csv`.
### Snakemake workflow
The entire workflow from raw spike files till the final figures is defined in `Snakefile` and `Snakefile_preprocessing`. If snakemake is installed, the figures can be produced by executing `snakemake`.
