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Homeostatic synaptic plasticity (Rabinowitch and Segev 2006a,b)

modeldb.science/114355

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Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
cells		cells
data_structure		data_structure
gui		gui
main		main
matlab		matlab
mechanisms		mechanisms
records		records
simulations		simulations
synapses		synapses
Simulations8.xls		Simulations8.xls
about.txt		about.txt
mosinit.hoc		mosinit.hoc
readme.html		readme.html
screenshot1.jpg		screenshot1.jpg
screenshot2.jpg		screenshot2.jpg
shapeplot.ses		shapeplot.ses

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<html><pre>
This is the readme for the model associated with the paper

Rabinowitch I, Segev I (2006) The interplay between homeostatic
synaptic plasticity and functional dendritic compartments. J
Neurophysiol 96:276-83

These files were supplied by Dr Ithai Rabinowitch.

The basic idea is:

1. Each simulation is given a RIP number and each RIP has several
   RDPs. RIP is a list of run-independent parameters such as the type
   of active channels on the dendrites. RDP is a list of run-dependent
   parameters (e.g. the simulation time). This allows you to set up a
   general RIP configuration and then run several RDP variations on
   it. The RIP and RDP parameter panels are at the top left.

2. Even above the RIP category is the neuron structure and channel
   file which are selected just before entering the main gui.

3. There are several types of simulation programs such as EPSP (which
   measures individual EPSP amplitudes for each synapse). These are
   chosen in the panel in the bottom.

4. It is possible to pre-program the simulation to run several
   simulations in sequence (if you want to leave the computer to work
   overnight and run different simulations one after the other).

Usage:

Download and extract the archive.  Then under

unix/linux:
-----------

cd main
nrnivmodl ../mechanisms
nrngui main.hoc

In the first selection window choose Spruston2 (not 3) and in the
Migliore2 Channel layout and Segment length 20.

<img src="./screenshot1.jpg" alt="screenshot 1">

Then click 'Done'.

You will be able to get 6 simulation configurations (RIP0: RDP0-5)
that do the following (the simulations are quite long):

RDP 0: runs in 'frozen' mode, i.e. no plasticity. This is used to get
a profile of the average membrane potential at each dendritic site (at
the end of the simulation choose Vavg in one of the two plot windows).

RDP 1: runs with plasticity so that at the end you also get gmax
values that are different from gmax0

RDP 2-5 start with the gmax distribution of RDP1 (since I have already
run this, their gmax0 is supposed to be stored).

RDP 2: local HSP RDP 3: frozen with the gmax0 obtained from RDP2's
final gmax.

RDP 4: global HSP RDP 5: frozen with the gmax0 obtained from RDP4's
final gmax.

---

Select "artificial vivo", click "add" and "go". While it is running
you can select Interaction -> distance -> gmax and Interaction ->
distance -> vmax in the graph windows, then your simulation will look
like this:

<img src="./screenshot2.jpg" alt="screenshot 2">

I would suggest that you create a new RDP and just set a much shorter
simulation time (TSTOP under the RDP list). You can then run it to
make the result files (under for example
./records/files/ri05-Migliore2-seg-1-20/RIP-0/RDP-0/ ) accessible
without having to run the whole simulation. If you want interesting
things to happen in the short time, you can change the time constant
of the plasticity mechanism. Create a new RIP configuration (or delete
the existing one) and change the time scale parameter in the synapse
parameter dialog box (just under the RIP list).

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