From e0be3e2970e05bf081b7aed0f8e5c222c9410583 Mon Sep 17 00:00:00 2001 From: Maximilian Schmidt <max.schmidt@fz-juelich.de> Date: Wed, 30 May 2018 14:21:44 +0900 Subject: [PATCH] Update README file with more info on new simulations --- figures/Schmidt2018_dyn/README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/figures/Schmidt2018_dyn/README.md b/figures/Schmidt2018_dyn/README.md index fe20bf1..bc6bd07 100644 --- a/figures/Schmidt2018_dyn/README.md +++ b/figures/Schmidt2018_dyn/README.md @@ -12,15 +12,15 @@ You can retrieve the original data from the Dryad Digital Repository database (T ### 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. +To work with newly simulated data, you first have to run the necessary simulations. In `network_simulations.py`, we define the parameter dictionaries for all simulations along with data structures associating simulations with the respective figures. To run the simulations for a specific figure, execute the `run_simulations(figure)` (set `all` for all figures and e.g. `Fig2` for figure 2). Please note that you will need to provide sufficient resources on an HPC cluster. +You then have to set `LOAD_ORIGINAL_DATA = False` in the `Snakefile` and the respective plot scripts to switch 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`. +Figure 8 requires the experimental fMRI data (described by Babapoor-Farrokhran et al. (2013), see Methods section of Schmidt et al. 2018 for more details) that are contained in this repository in `Fig8_exp_func_conn.csv`. ### Snakemake workflow -- GitLab