Models of layer 5 pyramidal neurons.
Python
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hoc
mod_hay
mod_traub
morphology
Hay.hoc
LICENSE
README.org
Traub.hoc
current_compare.py
morph_compare.py
table_passive.org
viz_cond.py

README.org

Here we compare existing neocortical layer 5 pyramidal cells from modeldb

Requirements

neuron simulator (compiled with pyneuron)

matplotlib

numpy

Models currently tested for

  1. Traub et.al. - tuft IB Pyramidal cell - 2005
  2. Hays et.al. - BAC firing model - 2011

In future

  1. Mainen et.al. - 1996
  2. Larkum et.al. - 2009
  3. Kole et.al. - 2008

To start

You will need to compile the mod files.

> nrnivmodl mod_hay/

if you want to run the Hay cell model or

>nrnivmodl mod_traub/

if you want to run the Traub cell model

[TODO] Having to compile each time user wants to run the scrips is annoying - find a better way to do this.

What do the scripts do?

morph_compare.py

Usage

> python morph_compare.py [option1$] [option2]

$ - necessary

Available option1 - Model name

‘Hay’

‘Traub’

Available option2 - To show in matplotlib or not?

True (default)

False

Does what?

Shows the morphology of the cell in matplotlib 3D.

Prints the following in terminal

  1. the number of segments and sections
  2. the area of the cell
  3. length of the cell

viz_cond.py

Usage

> python viz_cond.py [option1$]

$ - necessary

Available option1

‘Hay’

‘Traub’

Available option2

‘g_pas’ (default)

‘cm’

etc.

Does what?

Shows the colormapped morphology of a given parameter in 3D.

This script is useful to map the channel conductances over the cell body

current_compare.py