Using analyseur to analyze rBCBG data

The rBCBG Model is available here

Regardless of how one sets up the simulation, to use this analyseur tool

Example simulation pipeline

1. Get (Go to) the model

Get the model that has been prepared of graded disinhibition (disinhibition-experiments branch)

git clone -b disinhibition-experiments ssh://git@gitlab.isir.lan:2222/cobathaco-catatonia/bcbg-parents/rBCBG-ANNarchy.git
cd rBCBG-ANNarchy

2. Create a shell script for batch run

from core import multirun

decaylist = [0, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50,
             0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.0]

results = multirun(decaylist)

3. Structure of stored results

Running the multirun will automatically create a subdirectory decay such that its sub-folder structure will look like

.
├── 0/
│   ├── CTX_I_model_<ID>_percent_0.csv
│   ├── CTX_E_model_<ID>_percent_0.csv
│   ├── CSN_model_<ID>_percent_0.csv
│   ├── FSI_model_<ID>_percent_0.csv
│   ├── GPe_model_<ID>_percent_0.csv
│   ├── GPiSNr_model_<ID>_percent_0.csv
│   ├── MSN_model_<ID>_percent_0.csv
│   ├── PTN_model_<ID>_percent_0.csv
│   ├── STN_model_<ID>_percent_0.csv
│   ├── TH_model_<ID>_percent_0.csv
│   └── TRN_model_<ID>_percent_0.csv
├── 1/
│   ├── CTX_I_model_<ID>_percent_1.csv
│   ├── CTX_E_model_<ID>_percent_1.csv
│   ├── CSN_model_<ID>_percent_1.csv
│   ├── FSI_model_<ID>_percent_1.csv
│   ├── GPe_model_<ID>_percent_1.csv
│   ├── GPiSNr_model_<ID>_percent_1.csv
│   ├── MSN_model_<ID>_percent_1.csv
│   ├── PTN_model_<ID>_percent_1.csv
│   ├── STN_model_<ID>_percent_1.csv
│   ├── TH_model_<ID>_percent_1.csv
│   └── TRN_model_<ID>_percent_1.csv
├── ...
├── ...
├── N/
    ├── CTX_I_model_<ID>_percent_N.csv
    ├── CTX_E_model_<ID>_percent_N.csv
    ├── CSN_model_<ID>_percent_N.csv
    ├── FSI_model_<ID>_percent_N.csv
    ├── GPe_model_<ID>_percent_N.csv
    ├── GPiSNr_model_<ID>_percent_N.csv
    ├── MSN_model_<ID>_percent_N.csv
    ├── PTN_model_<ID>_percent_N.csv
    ├── STN_model_<ID>_percent_N.csv
    ├── TH_model_<ID>_percent_N.csv
    └── TRN_model_<ID>_percent_N.csv

where

  • respective terminal folder 1/, 2/, …, N/ contains many csv files that stores firing rates data of respective nucleus.

    • the data is an array with shape (time_to_simulate, <region>_neurons)

    • for example (9999, 1) for the basal ganglia neurons and (9999, 24) for the thalamic neurons

Scripts

Scripts: