About | Technologies | Getting Started | License | Author | Acknowledgement
Neural activity is simulated at different levels of biological detail, and to make experimentally testable predictions it should be possible to calculate measurable brain signals from these simulations. However, simulations using simplified representations of neurons (levels II and III in the figure below) are often not in a principled way able to predict brain signals like LFP, EEG, or MEG signals. The motivation for this usecase is to enable calculation of LFP, EEG, and MEG signals directly from neural simulations with point neurons (like in NEST), or firing rate models (like in TVB).
We used the cortical microcircuit model by Potjans and Diesmann, available from https://nest-simulator.readthedocs.io/en/stable/auto_examples/Potjans_2014/
The LFP signals are calculated from the spike events by applying the so-called kernel approach, as outlined in Hagen et al. (2022): https://doi.org/10.1371/journal.pcbi.1010353
This usecase can be used as a starting point for applying the Co-simulation framework to other network models in NEST or TVB, and also for simulating other brain signals like EEG, MEG, or ECoG signals.
The following tools were used in this project:
The Modular Science Co-simulaiton framework and usecase can be installed and launched on:
- Local systems: e.g. a virtual machine (VM) on a laptop. We support the useage of Virtualbox and Vagrant.
Please check HERE for installation details.
The framework and usecase can be launched in two different following ways:
- From within the cloned repo:
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go to run_usecase/local directory and run this script from there e.g.
vagrant@ubuntu-focal:~multiscale-cosim/Cosim-LFPy/run_usecase/local$ sh ./run_on_local.sh
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- From outside of the cloned repo:
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On the VM (see Installation guide above) you will find two following scripts in
/home/vagrant/multiscale-cosim:Cosim-LFPy.sourceandrun_on_loacl.sh
run them as following:
vagrant@ubuntu-focal:~multiscale-cosim$ source Cosim-LFPy.source vagrant@ubuntu-focal:~multiscale-cosim$ ./run_on_loacl.sh
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Simulation Results: The simulation results, logs, and the resource usage stats can be found in directory Cosimulation_outputs created by Modular Science during the execution at the same location where the execution script is run.
This project is under license from Apache License, Version 2.0. For more details, see the LICENSE file.
Made by Multiscale Co-simulation team.
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 785907 (HBP SGA2), from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (HBP SGA3) and from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3)