CA1 pyramidal neuron: synaptically-induced bAP predicts synapse location (Sterratt et al. 2012)

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Accession:144490
This is an adaptation of Poirazi et al.'s (2003) CA1 model that is used to measure BAP-induced voltage and calcium signals in spines after simulated Schaffer collateral synapse stimulation. In the model, the peak calcium concentration is highly correlated with soma-synapse distance under a number of physiologically-realistic suprathreshold stimulation regimes and for a range of dendritic morphologies. There are also simulations demonstrating that peak calcium can be used to set up a synaptic democracy in a homeostatic manner, whereby synapses regulate their synaptic strength on the basis of the difference between peak calcium and a uniform target value.
Reference:
1 . Sterratt DC, Groen MR, Meredith RM, van Ooyen A (2012) Spine calcium transients induced by synaptically-evoked action potentials can predict synapse location and establish synaptic democracy PLoS Comput Biol 8(6):e1002545 [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:
Cell Type(s): Hippocampus CA1 pyramidal cell;
Channel(s): I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I Mixed; I R; I_AHP;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Synaptic Plasticity;
Implementer(s): Sterratt, David ; Groen, Martine R [martine.groen at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell; AMPA; NMDA; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I Mixed; I R; I_AHP;
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bpap
CA1_multi
datastore
pars
plots
poirazi-nmda-car
tests
validation-plots
README.txt
ampa_forti.mod
cacum.mod
cad.mod *
cagk.mod
cal.mod
calH.mod
car.mod
car_mag.mod
cat.mod
d3.mod *
h.mod
hha_old.mod
hha2.mod
kadist.mod
kaprox.mod
kca.mod
km.mod
nap.mod
nmda_andr.mod
somacar.mod
binaverages.m
bpap-cell.hoc
bpap-data.hoc
bpap-dendburst.hoc
bpap-graphics.hoc
bpap-gui.hoc
bpap-gui.ses
bpap-pars.hoc
bpap-record.hoc
bpap-run.hoc
bpap-scaling.hoc
bpap-sims.hoc
bpap-sims-cell1.hoc
bpap-sims-cell2.hoc
bpap-sims-scaling.hoc
bpap-somainj.hoc
bpap-spiketrain.hoc
ca1_mrg_cell1.hoc
ca1_mrg_cell2.hoc
ca1_poirazi.hoc
ChannelBlocker.hoc
CrossingFinder.hoc
epspsizes.hoc
figure-example.R
figures.R
figures-common.R
FileUtils.hoc
FormatFile.hoc
ghk.inc
GraphUtils.hoc
Integrator.hoc
Makefile
mosinit.hoc
NmdaAmpaSpineSynStim.hoc
NmdaAmpaSynStim.hoc
ObjectClass.hoc
plotscalingresults_pergroup1.m
plotscalingresults5.m
PointProcessDistributor.hoc
ReferenceAxis.hoc
removezeros.m
RPlot.hoc
scaling_plots.m
Segment.hoc
SimpleSpine.hoc
Spine.hoc
TreePlot.hoc
TreePlotArray.hoc
triexpsyn.inc
units.inc
utils.hoc
validate-bpap.hoc
VarList.hoc
VCaGraph.hoc
                            
DDSP README file
================

David Sterratt, 4th July 2012
-----------------------------

How to run the simulations interactively
========================================

1. Compile all the ".mod" files in this directory using
   the NEURON utility "nrnivmodl" (on GNU/Linux) or mknrndll (on MS
   Windows).

2. Use NEURON to run "bpap-gui.hoc". A number of windows should appear
   on the screen. This is the interative version of the simulations.

3. Change parameters and options as desired, and then click on "BPAP
   Run". For example, try setting "AMPA synapses scaled", and changing
   the "Number of runs" to 5.

4. The simulation will run. Traces appear in the window at the right,
   and various analysis plots will appear in the centre window. The
   top row refers to voltage, and the bottom row to calcium. The left
   column is peak V or Ca, the middle column is integral of V or Ca
   and the right column is time to peak V or Ca.

5. To save the parameters and data, click on "Save Parameters and
   Data". Click on "Accept" in the window that pops up, and the data
   and parameters will be saved in a file in R format in the datastore
   directory.

6. To plot figures from this file, open up the R program, and type the
   following at the prompt:

   > source("figure-example.R")

   The first time this happens you may be prompted to download a
   package - this is intended.

7. To produce further simulations and plots, repeat steps 3 to 6. You
   will need to copy "figure-example.R" to a file with a new name and
   edit the "dataset" line to match the name of the dataset in the
   datastore directory.

How to reproduce the simulations with the standard morphology
=============================================================

1. Compile the mod files as in step (1) above.

2. Use NEURON to run "bpap-sims.hoc". This will take some time. Data
   files (R text files) will appear in the "datastore" directory.

3. To produced the figures, start R and type:

   > source("figures.R")

   Figures will appear in the "plots" directory.

How to reproduce the scaling simulations
========================================

1. Compile the mod files as above.

2. Use NEURON to run "bpap-sims-scaling.hoc". This will take some
   time. Data files (text files with a .dat suffix) will appear in the
   "datastore" directory.

3. Open MATLAB from the bpap directory and type "scaling_plots"

To run simulations with cells with alternative morphologies (Fig 3B,C)
======================================================================

1. Compile the mod files as above.

2. Use NEURON to run "bpap-sims-cell1.hoc" and
   "bpap-sims-cell2.hoc". This will take some time. Data files (R text
   files) will appear in the "datastore" directory.

3. These can be plotted using figure-example.R



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