Brian implementation of synaptic plasticity (calcium-induced, with synaptic tagging and capture) in neuronal networks
This code implements a single current-based synapse which can undergo early-phase plasticity based on calcium dynamics and late-phase plasticity based on synaptic tagging and capture.
The early-phase dynamics are driven by neuronal spiking activity, and the late-phase dynamics depend on the early-phase through tag setting and protein synthesis (see Luboeinski and Tetzlaff, 2021, for details).
The simulation reproduces the outcome of a stand-alone simulator (see this repo) and of the Arbor simulator (see this repo).
First of all, Brian 2 needs to be installed:
pip install brian2
To run the simulations and average over trials and batches, execute
python3 runBatchesBasic.py
To plot the results produced by the previous step, execute
python3 plot.py
Alternatively, you can run batches of early- or late-phase simulations, respectively, via
source run_batch_basic_early
source run_batch_basic_late
To run a single simulation of early- or late-phase dynamics, execute, respectively
source run_one_trial_early_phase
source run_one_trial_late_phase
For tests and to obtain the line coverage, pytest and coverage.py need to be installed:
pip install -U pytest pytest-cov coverage
To run tests and determine the test coverage for the main module, execute
source run_tests
Averaged over 10 batches with 100 trials each, the mean across batches is shown (computed from the mean across trials); error bands show the standard deviation across batches.
Averaged over 10 batches with 10 trials each, the mean across batches is shown (computed from the mean across trials); error bands show the standard deviation across batches.
