Published June 3, 2026
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Publication data, notebooks and plots for Geminiani, Meier, Perdikis et al. publication
Authors/Creators
-
1.
Berlin Institute of Health at Charité - Universitätsmedizin Berlin
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2.
Champalimaud Foundation
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3.
Charité - Universitätsmedizin Berlin
Description
In order to run the notebooks, one has to mount this folder ("publication_data")
to the docker container running tvb-multiscale software and the scripts related to the study,
which can be found here (multiplatform - linux/arm64 & linux/amd64 - manifest):
https://hub.docker.com/repository/docker/dionperd/tvb-multiscale-dev/tags/rising-net_publication/sha256:511c1be7209e0966948a588ca4f450932054e985dc17af96dc5830fa3c9c04aa
(Index digest: sha256:511c1be7209e0966948a588ca4f450932054e985dc17af96dc5830fa3c9c04aa)
Ideally, the folder should be mounted to the following path inside the container:
"/home/docker/packages/tvb-multiscale/rising_net/publication_data"
You could run then the docker image with the following command
(as long as you substitute for your own path "/your/local/path/to/publication_data"):
docker run \--name rising_net_publication \-p 8888:8888 \-v /your/local/path/to/publication_data:/home/docker/packages/tvb-multiscale/rising_net/publication_data \dionperd/tvb-multiscale-dev@sha256:511c1be7209e0966948a588ca4f450932054e985dc17af96dc5830fa3c9c04aa \/home/docker/.local/bin/jupyter-notebook --ip 0.0.0.0 --no-browser --allow-root
Then go to you browser at localhost:8888 and use the password "tvb42" to enter,
navigate to /home/docker/packages/tvb-multiscale/rising_net/publication_data and run the notebooks!
(All references to figures' and tables' labels in parentheses below correspond to the initial paper submission.)
Contents' description
FIT_REST
Data and notebooks with results of fitting parameters without any task specific dynamics
(see Supplementary Table S4, Supplementary Note 1, Supplementary Figure S7 and Methods 4.2.2 of the main manuscript)
./round_1/plot_S7fig_FIT_REST.ipynb
Notebook to produce Supplementary Figure S7
FIT_TASK
Data and notebooks with results of fitting task specific parameters
(see Supplementary Table S5, Supplementary Note 1, Supplementary Figure S8 and Methods 4.1.5 of the main manuscript)
./round_0/plot_S8fig_FIT_TASK.ipynb
Notebook to produce Supplementary Figure S8
wTVBtoNEST
./wTVB_to_NEST.ipynb
Notebook exemplifying the grid search for the TVB to NEST interface tuning
and for generating relevant data of Supplementary Table S7
(see also Supplementary Note 1 and Methods 4.4 of the main manuscript)
./wTVB_to_NEST_confirmation.ipynb
Notebook to confirm the mean population rate of Ansiform Lobule granule cells after tuning TVB - NEST interfaces.
wNESTtoTVB
Data and notebooks to load and print the parameters of the tuned NEST to TVB interfaces
./wNESTtoTVB.ipynb
Notebook to load and print the parameters of the tuned NEST to TVB interfaces.
It generates contents of Supplementary Table S7
(see also Supplementary Note 1 and Methods 4.4 of the main manuscript)
Final10reps
Data and notebooks to confirm both the mean population rate of Ansiform Lobule granule cells
and the M1-S1 coherence drop effect upon deactivation of the cerebellum.
./plot_S9fig_GrCrates.ipynb
Notebook to generate Supplementary Figure S9
conn_coherence_drop_plot
Notebooks generating figures of connectivity and coherence drop between CEREBON and CEREBOFF conditions
./plotting-connectivity-matrix.ipynb
Notebook generating the plot of the connectivity matrix used for simulations (Figure 1, panel A).
./plotting_coherence_drop.ipynb
Notebook generating plots of coherence drop between CEREBON and CEREBOFF conditions
(Figure 2, panels D & E and Supplementary Figure S2).
analysis_notebooks
Notebooks performing analysis of PSD, lesions, spike's and spikes' synchronization metrics and generating related plots.
./PSD_plot/PSD_plot.ipynb
Notebook loading and ploting M1 and S1 PSD in various simulation conditions (TVMB-only and CO-SIM, cerebON and cerebOFF;
Figure 2, panels A-C and Supplementary Figure S1).
./spikes_analysis/spikes_analysis/ipynb
Notebook loading and ploting spike trains from one example CONTROL co-simulation, as rasterplots, spike histograms and average firing rates (Figure 2, panel F).
./lesion_analysis/lesion_analysis.ipynb
Notebook loading and ploting PSD and coherence data from CONTROL co-simulations and various lesion conditions (inputs to DCN and MLI lesions; Figures 3 & 4 and Supplementary Figures S4, S5 & S6).
./spike_synch_analysis/spike_synch_analysis/ipynb
Notebook loading and ploting spike analysis and synchronization measures from CONTROL co-simulations and various lesion conditions (inputs to DCN and MLI lesions; Figures 5 & 6 and Supplementary Figures S7 & S8).
Files
publication_data.zip
Additional details
Software
- Repository URL
- https://github.com/virtual-twin/tvb-multiscale-rising-net/releases/tag/Geminiani_Meier_Perdikis_etal
- Programming language
- Python
- Development Status
- Active