Network simulation using Brian 2 and Pypet written to analyse the survivability of transient synapses of cortical neurons.
To run the network simulation a Python 3 environment with Brian 2, and Pypet is required. Git also has to be installed.
Any recent version of Brian 2 should work. However, to run very long simulations a fix discussed in #1057 is required.
Below is an example installation routine for setting up a virtualenv (tested on Ubuntu 16.04 only).
#!/bin/sh
virtualenv -p python3 /home/$USER/env/synsrv
source /home/$USER/env/synsrv/bin/activate
# Brian 2 branch that fixes bug for long simulations
pip install -e git+https://github.com/brian-team/brian2@355cbf98061f2ae4c4afdc1600f363c5d8c0979d#egg=Brian2
pip install mrestimator==0.1.5
pip install elephant==0.6.0
pip install tables==3.5.1
pip install pypet==0.4.3
pip install GitPythonGet the code from this repository including submodules with
git clone --recurse-submodules https://github.com/synsrv/src_net
To verify your installation, within src_net run
./run_test.sh -l tests/net_tests/test_standard_net/This will create a directory tests/ on the same level as src_net where the code is copied an executed.
To run simulations exploring different parameter sets, create an explored_params.py in src_net/net/, as for example found in any of the tests in net_tests/. In the input_dict of explored_params.py specify the parameter setting of your choice and the runn simulation via
./run.sh -l -n 2 -P "_two-concurrent-sims" -E
This will create running/ and completed/ directories on the same level as src_net/. Once finished, the simulation directory is moved from running/ to completed/.