# Quickstart¶

## Package structure¶

These are the directories of the package:

• biochemical_circuits contains all the biochemical network which have been used at different stage of the development of the model.
• branch_dist contains the code to calculate the spine distribution as explained in the paper and in the thesis
• ecellControl is the module with the ecellManager class, which controls the E-Cell simulator and it’s used ae entry-point in the main synchronization script (spineIntegration.py)
• helpers is a directory where there are some utilities script used to plot and explore the data
• hoc contains the hoc file to instantiate the MSN without any spines based on the model of
• mod contains the NMODL file which needs to be compiled and than can be loaded into section in the Neuron model.
• neuroControl is the module with the NeuronManager class, which is used to control NEURON. In this module there are also the class to create the hybrid spine, which has both electrical and biochemical nature.
• param contains the parameters file used to run the simulations.
• spineIntegration.py is the main script which runs the multiscale model.
• extref.py contains the class to extend Neuronvisio storage format to accept the biochemical results on top of the electrical one.
• visioStart.py instantiate the model and loads it in the Neuronvisio software.

## Dependencies¶

### Ecell¶

To run the model you need to install E-cell3 (3.1.106) version, which you can download from https://sourceforge.net/projects/binaryfiles/files/latest/download and compile it with the python support.

### Neuron¶

Neuron is available from http://www.neuron.yale.edu/neuron/, and it has to be compiled with python support

### Neuronvisio¶

Neuronvisio is needed to save the simulation and can be obtained from http://neuronvisio.org/

## Running the model¶

To run the model you need to run it as:

python spineIntegration.py parameter_file.param

where the parameter_file.param is the file you want to use to run the model.

In the params directory there are the files to run the model in different ways:

The most important parameters are:

1. spines_dist, which can be:
1. zero for no spines

2. two for only two spines

3. onebranch to instantiate all the spines in one branch (one medial and two distal

dendrites)

4. all to instantiate all the spines

2. bio_on If True the biochemical integration will be used, if False

no biochemical integration will be used (If you are only interested in the electrical behaviour set it to False).

For example to run a the model with just two spines, for a very short time do:

python spineIntegration.py param/two_spines_stim.param

To run a longer period, do:

python spineIntegration.py param/long_tstop_double_stim_two_spines.param

If you want to run the model with all the spines, you can run (this is very big. I’ve ran it with 60GB of RAM on the EBI Cluster:

python spineIntegration.py param/long_tstop_allbranch_cpm_two_branches_stims_20_Hz.param

An example of how to run the model using only the electrical part is possible with the param file:

python spineIntegration.py param/short_tstop_electrical.param