Stochastic layer V pyramidal neuron: interpulse interval coding and noise (Singh & Levy 2017)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:237594
Layer V pyramidal neuron with stochastic Na channels. Supports evidence for interpulse interval coding and has very detailed AIS with Nav1.2 and Nav1.6 channels.
Reference:
1 . Singh C, Levy WB (2017) A consensus layer V pyramidal neuron can sustain interpulse-interval coding. PLoS One 12:e0180839 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation;
Implementer(s): Singh, Chandan [chandan_singh at berkeley.edu];
# running
- the files in the mechanism folder need to compiled by NEURON
- use the NEURON gui to launch the file mechanism/run_act.hoc
- this will run the code with a current injection and save data on channels in the AIS and voltages accross the neuron to the data folder

# overview
- the mechanism folder includes mod files for channels as well as the main running file
    - files with "_stoch" in the name are stochastic
- main.hoc initializes everything
    - the morphology folder includes files detailing the shapes of different axons
    - density_mechs.hoc distributes the passive and active conductances through the NEURON
    - inject_soma.hoc inserts an IClamp at the soma and runs the simulation
    - c.ses loads a gui for viewing the voltage over time
        - recording.hoc defines methods for recording / saving data
    - mechanism/run_act.hoc runs and displays an example action potential
- the model is largely based on: (Hu, et al. 2009): "Distinct contributions of Na v 1.6 and Na v 1.2 in action potential initiation and backpropagation.", which was itself built up through several studies
    - the main change is the change to stochastic Na channels	
    - other minor changes are described in the paper (Singh & Levy, 2017) "A consensus layer V pyramidal neuron can sustain interpulse-interval coding."
- part of model is based on
    - Mainen, Z. F. and Sejnowski, T. J.  Nature 382: 363-6 (1996)
    - Yu, Y., Shu, Y., et al.  J Neurosci 28: 7260-72 (2008)
    - Shu, Y., Hasenstaub, A., et al.  Nature 441: 761-5. (2006)
    - Kole MH, Hallermann S, Stuart GJ (2006) J Neurosci 26:1677-87