hbp-cerebellum-models

Package of Human Brain Project (HBP) Cerebellum models.

Description

This repository contains cerebellum models developed by the cerebellum team led by Prof. Egidio D’Angelo at the Human Brain Project.

Table of Contents

Installation

Dependant packages (versions based on 31 August 2017):

• NEURON (tested on Release 7.4 (1370:16a7055d4a86) 2015-11-09)
• Numpy (tested on 1.11.0)
• NEO (tested on 0.5.1)
• Elephant (tested on 0.4.1)
• Quantities (tested on 0.12.1)
• Matplotlib (tested on 1.5.1)

Usage

1. To start using first:

git clone https://github.com/lungsi/hbp-cerebellum-models.git
cd hbp-cerebellum-models

2. To see the models import the model_manager module

from models import model_manager as mm

The models in the hbp-cerebellum-models pack are broken down into three model_scale: cells, microcircuit and network.

To see the names of the cellular models use the model_manager.get_available_models function

mm.get_available_models( model_scale="cells" )

3. Instantiate a model, say, the cellular model, PC2015Masoli first import the cells module

from models import cells

Then instantiate the model

pc = cells.PC2015Masoli.PurkinjeCell()

Note: PC2015Masoli is a Purkinje cell. For GrC2001DAngelo which is a Granular cell use the command: grc = cells.GrC2001DAngelo.GranularCell()

4. Run the instantiated model

   • The default voltage response

     pc.produce_voltage_response()
     

     This is the same as

     pc.produce_voltage_response( cell_regions=['vm_soma', 'vm_NOR3'])
     

     NB: NOR3 stands for 3rd Node of Ranvier.

   • The default spike response

     pc.produce_spike_train()
     

     This is the same as

     pc.produce_spike_train( cell_locations=['vm_soma'], thresh=[0.0] )
     

     NB: Non default example pc.produce_spike_train( cell_locations=['vm_soma', 'NOR3'], thresh=[0.0, -1.0] )

5. To visualize the results first import the plot_manager module

from models import plot_manager as pm

Then to visualize the spikes

pm.visualize_spikes( model_name="PC2015Masoli", region_of_interest="vm_soma" )

or visualize the voltage response

pm.visualize_voltages( model_name="PC2015Masoli", region_of_interest="vm_soma" )

Contribution

Credits

License

BSD-3-Clause Copyright 2017 Lungsi See LICENSE.txt