Pyramidal neuron conductances state and STDP (Delgado et al. 2010)

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Accession:144482
Neocortical neurons in vivo process each of their individual inputs in the context of ongoing synaptic background activity, produced by the thousands of presynaptic partners a typical neuron has. That background activity affects multiple aspects of neuronal and network function. However, its effect on the induction of spike-timing dependent plasticity (STDP) is not clear. Using the present biophysically-detailed computational model, it is not only able to replicate the conductance-dependent shunting of dendritic potentials (Delgado et al,2010), but show that synaptic background can truncate calcium dynamics within dendritic spines, in a way that affects potentiation more strongly than depression. This program uses a simplified layer 2/3 pyramidal neuron constructed in NEURON. It was similar to the model of Traub et al., J Neurophysiol. (2003), and consisted of a soma, an apical shaft, distal dendrites, five basal dendrites, an axon, and a single spine. The spine’s location was variable along the apical shaft (initial 50 μm) and apical. The axon contained an axon hillock region, an initial segment, segments with myelin, and nodes of Ranvier, in order to have realistic action potential generation. For more information about the model see supplemental material, Delgado et al 2010.
Reference:
1 . Delgado JY, Gomez Gonzalez JF, Desai NS (2010) Pyramidal neuron conductance state gates spike-timing-dependent plasticity J. Neurosci. 30(47):15713-25 [PubMed]
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: Auditory cortex;
Cell Type(s): Neocortex V1 pyramidal intratelencephalic L2-5 cell;
Channel(s): I Na,p; I Sodium; I Calcium; I Potassium; I_AHP;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potentials; STDP; Calcium dynamics; Conductance distributions;
Implementer(s): Gomez-Gonzalez, JF [jfcgomez at ull.edu.es]; Delgado JY, [jyamir at ucla.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal intratelencephalic L2-5 cell; AMPA; NMDA; I Na,p; I Sodium; I Calcium; I Potassium; I_AHP;
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Pyramidal_STDP_Gomez_Delgado_2010
experiment
mechanism
morphology
readme.txt
mosinit.hoc
                            
NEURON PROGRAM FOR SIMULATING PYRAMIDAL NEURON CONDUCTANCES STATE AND STDP

Delgado JY, G�mez Gonz�lez JF, Desai NS. Pyramidal neuron conductance
state gates spike-timing-dependent plasticity. J Neurosci. 2010 Nov
24;30 (47):15713-25.  doi: 10.1523/JNEUROSCI.3068-10.2010

Folders:

"..\morphology\" : contains the morphology of the model cell 
"..\mechanism\"  : contains mechanisms of the model cell 
"..\experiment\" : contains experiments and data of simulations 


Instructions:

0- Auto-launch from ModelDB and skip to step 3 or:
1- Copy all the folders into your computer.
2- To Compile the mechanisms, you have to execute "clean-compile.bat"
file in folder "..\mechanism\mechanism_cell1\" (for mswin).  For
linux/unix compile the mod files with nrnivmodl.
3- Simulations:    

   a) Execute "run.hoc" from "..\experiment\" folder.
   b) Fit the morphology variable (diameter and length of dendrites
   and soma, position and morphology of the spine) and parameters of
   the mechanisms, etc, if it was necessary.
   c) There are two options to run:
          i) One run: Press the "Run" key, in this case, it executes
          one simulation. If you wanted to save the data, you have to
          select a "Number of Folder", for example "1", and if you
          press the key "Save", the data will save in
          "..\experiment\data_1".

          ii) Multi-runs: Press the "Auto Runs" key, in this case, it
          executes multiple simulations. The number of runs is given
          in "..\experiment\Protocols.hoc" file, in addition, it is
          able to define the protocols that you want to apply for
          every run. By default, Delgado et al, 2010 defined the
          position from the spine to the soma for every run. The data
          will save automatically into folders named "data_XX", XX is
          the distance from the spine to the soma.


For questions:
Jos� Francisco G�mez Gonz�lez, jfcgomez@ull.edu.es

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