Continuous Create gives you an extra degree of flexibility. If the Continuous Create button is checked, changes are passed from the CellBuilder to the interpreter as they occur, without anything being written to an output file. This means that you can immediately explore the effects of anything you do with the CellBuilder.
Try the following steps to see how this works.
1. Use nrngui
to start NEURON from an xterm or DOS window
in the course/ballstk directory.
2. Bring up the CellBuilder. Look at the Management page to make sure that Topology, Subsets, Geometry, and Biophysics are checked, and then toggle Continuous Create ON.
3. Build a cell that looks like this:
Use any anatomical and biophysical properties you like; these might be interesting to start with:
Section | L (um) | diam (um) |
soma | 30 | 30 |
trunk | 400 | 3 |
trunk[1] | 400 | 2 |
oblique | 300 | 1.5 |
tuft | 300 | 1 |
basilar | 300 | 3 |
topology()
and forall psection()
5. At the proximal end of tuft, place an alpha function synapse that has onset = 0 ms, tau = 1 ms, gmax = 0.01 umho, and e = 0 mV
6. Open a graph window to plot soma Vm vs. time. Also set up a space plot that shows Vm along the length of the cell from the distal end of the basilar to the distal end of the tuft.
7. Run a simulation. If necessary, increase Tstop until you can see the full time course of the cell's response to synaptic input.
8. Increase nseg until the spatial profile of Vm is smooth enough
(a couple of applications of
forall nseg *= 3
in the interpreter window should do the trick).
You may need to adjust the peak synaptic conductance in order
to trigger a spike.
Then use the command
forall print secname(), " ", nseg
to see how many segments are in each section.
9. You can also set nseg for any or all sections using the CellBuilder according to options that you select by Geometry/Specify Strategy. You can set the number of segments manually, or let the CellBuilder adjust them automatically according to one of these criteria:
Comments:
- Whether you choose d_lambda or d_X, the final value of nseg will be an odd number (this preserves the node at x = 0.5).
- Of these two options, d_lambda seems to have a more rational basis and may in general be preferable. "However, actual mileage may vary."
10. What happens if the sodium channels are blocked throughout the apical dendrites? Use the CellBuilder to reduce dendritic gnabar to 0 and then run a simulation.