Last updated: May 25, 2016
Before opening nrngui, make sure to compile code. Simulations can be run on desktop by opening the nrngui and loading the hoc file
promptWindow.hoc
##promptWindow promptWindow gives user access to control of all parameters for STDP experiments.
The location of these synapses can be set by the user from the dropdown menu. I have not set up synapse distribution throughout the entire cell simultaneously. Synaptic density should be as follows:
soma = 12.5 / um^2
prox = 0.1334 / um^2
midd = 0.009 / um^2
dist = 0.0025 / um^2
By default synapses are in the proximal dendrites.
Start of Paried Synapse Spikes determines the onset of plasticity induction. Paired synapses are GABAergic synapses which are pseudo-randomly distributed (per random synapse distribution seed, by default set as 37264 for no particular reason). They are "paired" with current clamp activity -- i.e. the clamp is set to start within some delta_t of the start of paired synapse spikes. (The delta_t value, inconveniently, is set in the mosinit files, in the procedure add_timestep().) To modify the delta_t value i.e. the time betweeen pre- and post-synaptic inputs, edit the correct mosinit file. If data is not recorded (default setting in promptWindow), the "Create Cell" button executes
mosinit_RUNonly.hoc
If data is to be recorded (not recommended for desktop runs -- intended to be run on SciNet on large memory nodes), the "Create Cell" button executes
mosinit.hoc
In both files, delta_t value can be modified by changing the value to be appended to timesteps, i.e.:
proc add_timestep(){
timesteps.append(5)
}
add_timestep()You can ignore the Unpaired Synapses block. These basically function the same as the paired synapses. I have set the density to 0 because we're not using them right now. (They are if you want to have one set of synapses activated coincidently with the clamp, and another set activated non-coincidently with the clamp. This was originally to try to replicate results from Woodin & Ormond 2010.)
For the standard induction protocol, the defaults should be
Current clamp amp = 3 (nA)
Current clamp dur = 5 (ms)
Interval between clamp events = 200 (ms)
Number of Clamp events = 150
Change only if you want new synapse distribution. The default number is totally random.
Checking the "Record Data" box is not recommended for desktop simulation runs. This causes "Create Cell" to call mosinit.hoc, which calls for significant memory allocation to record variables after the simulation run. Leaving "Record Data" unchecked calls mosinit_RUNonly.hoc, which does not require any memory allocation. Aside from data recording, mosinit.hoc and mosinit_RUNonly.hoc are identical in the hoc files they call.
The tree is as follows:
promptWindow.hoc
mosinit_RUNonly.hoc (or mosinit.hoc)
setParameters.hoc
makeCell.hoc
makeGeometry.hoc
makeIons.hoc
makeTransporters.hoc
makeActiveChannels.hoc
makePairedUnpaired.hoc
makeWindows.hoc
Clicking "Create Cell" will generate all of the windows necessary to play with the model specified by the user in the promptWindow. Simulation is run from RunControl window.
By default, plasticity induction is started ~ 10000s after the simulation begins, and is carried out at 5Hz for 30000 ms with clamp amp and duration at 3nA and 5ms, respectively (this protocol is a modified version of the plasticity induction protocol presented in Woodin et al., 2003). Plasticity induction parameters can be changed in promptWindow (Paired Synapses block). promptWindow defaults should generate the proper plasticity induction protocol.
Most other relevant parameters can be changed in setParameters.hoc. Changes to any hoc files can be implemented by clicking "Create Cell" again, without quitting NEURON all together. Changes to any mod files will require fully exiting NEURON, recompiling code (with nrnivmodl for Linux/UNIX or Mac, or the mknrndll applet with Windows), and reopening promptWindow.hoc.