Simulations that illustrate the firing pattern of a simulated dopamine
neuron in vitro and in vivo. These simulations are related to the
Canavier C.C. and Landry R.S. (2006) An increase in AMPA and a
decrease in SK conductance increase burst firing by different
mechanisms in a model of a dopamine neuron in vivo. J Neurophysiol
Example In Vivo Simulations
In these simulations, the file Receptor.cpp generates a random set of
Poisson-distributed events, and convolves the resultant pulse train
with the explicit solution to a differential equation that is a rising
exponential for the one ms that transmitter is postulated to reside in
the synaptic cleft, and a falling exponential thereafter. The
resultant .dat files are provided with each simulation. For example,
the files fig4bAMPA.dat and fig4bNMDA.dat drive the AMPA conductance
and NMDA permeability respectively for Fig.4B.
Note that the compiled mechanisms are different for nmda and ampa than
in the in vitro case because they are no longer constant, but rather
driven by the input files described above. You can run the simulation
either by auto-launching from ModelDB, or by first compiling the
mechanisms as follows:
Under linux: ---
Under Windows: ---
Run mknrndll twice to compile the mod files in the top level directory
and then in the in_vitro directory. Then double click on the
mosinit.hoc file to start the in vivo simulations or on the fig4a.hoc
to start the in vitro simulations.
Under MAC - OS X: ---
Drag and drop the archive file on the mknrndll icon (in the NEURON
application folder). Drag and drop the mosinit.hoc file onto the
Now that you have started the model on your platform:
Select a figure from the buttons and then press Init & Run.
Alternatively, if desired you can run the figures directly by running
commands under linux (with your path set appropriately):
special fig4b1.hoc -
Once the menu and graphics interface has appeared, click on the "Init
and run" button to start the simulation.
Follow the same instructions for the rest of the in vivo files:
fig4b2.hoc, fig4b3.hoc, fig5a.hoc, fig5b.hoc, fig9a1.hoc - fig9a3.hoc,
fig9b1.hoc - fig9b3, fig10a.hoc - fig10c.hoc, fig11b1.hoc, and
Note: two flags in the hoc files may be useful to the experienced
user. restart = 1 restarts from the initial conditions, whereas
restart = 0 does not, back = 0 uses the GUI, whereas back = 1 sends
the output to stdout.
Example In Vitro Simulation
These files simulates the bath application of glutamate in a slice
preparation such that the synaptic conductances reflect a constant,
average level of activation
You can run the simulation by first compiling the mechanisms as
In linux: ---
In windows: ---
Use mknrndll, change to the in_vitro, and make the nrnmech.dll there.
Double click the fig4a.hoc file.
In MAC - OS X: ---
Drag and drop the in_vitro folder onto the mknrndll icon in the NEURON
application folder. Drag and drop the fig4a.hoc file onto the nrngui
Now that the in vitro model is running:
Select a figure from the radio buttons. Once the menu and graphics
interface has appeared, click on the "Init and run" button to start