Warning

The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization. Future development will take place at: https://github.com/openbraininstitute/psp-validation

psp-validation

Validation of Post Synaptic Potentials (PSPs)

Installation

$ pip install psp-validation

Usage

Cli

The recommended usage is via the command line interface. To run simulations of psp with the test data:

psp run
    -c tests/input_data/simple/simulation_config.json \
    -t tests/input_data/simple/usecases/hippocampus/targets.yaml \
    -e default \
    tests/input_data/pathway.yaml \
    -o out \
    -n 1 \
    -r 1 \
    -j 1 \
    --dump-traces \
    --dump-amplitudes \
    --seed 400

-vv options stands for verbosity of log output. There are 3 different values for it:

• -v is for showing only warnings and errors
• -vv additionally to -v shows info messages
• -vvv additionally shows debug messages.

By default -v is used.

Somatosensory cortex (SSCx) example

After downloading the circuit model from Zenodo and creating out for simulation outputs

edit usecases/sscx/simulation_config.json and run:

psp -vv run
    -c usecases/sscx/simulation_config.json
    -t usecases/sscx/targets_v6.yaml
    -e S1nonbarrel_neurons__S1nonbarrel_neurons__chemical
    -o out/
    -n 50
    -r 35
    -j 35 usecases/sscx/pathways/primary/L5_TTPC-L5_TTPC.yaml.yaml
    --dump-traces
    --dump-amplitudes

which will sample 50 pairs of connected L5 thick thufted pyramidal cells from the circuit, trigger a single presynaptic spike from the presynaptic ones

and record the PSP on the postsynaptic ones. The process will be repeated 35 times (as synapses are stochastic and thus PSP varry in amplitude)

on 35 CPUs in parallel. It will saved the postsynaptic traces (to .h5), mean PSP amplitudes (to .txt) and a summary with a calculated conductance (g_syn)

scaling factor (to .yaml).

Testing

tox -e py310

Citation

If you use this software, kindly use the following BibTeX entry for citation:

@article{Ecker2020,
author = {Ecker, Andr{\'{a}}s and Romani, Armando and S{\'{a}}ray, S{\'{a}}ra and K{\'{a}}li, Szabolcs and Migliore, Michele and Falck, Joanne and Lange, Sigrun and Mercer, Audrey and Thomson, Alex M. and Muller, Eilif and Reimann, Michael W. and Ramaswamy, Srikanth},
doi = {10.1002/hipo.23220},
journal = {Hippocampus},
number = {11},
pages = {1129--1145},
pmid = {32520422},
title = {{Data-driven integration of hippocampal CA1 synaptic physiology in silico}},
volume = {30},
year = {2020}
}

Acknowledgements

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

This project/research received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).

For license and authors, see LICENSE.txt and AUTHORS.txt respectively.

Copyright (c) 2022-2024 Blue Brain Project/EPFL