Demo Files
Demo 1 for New simulation database) and Run it); fire IPSPs in another compartment
(select the Synaptic Firing Times command, press the Delete all firing times button, select another compartment and synapse with the compartment popup menu (third from the left), type in the Firing times, press OK, do New Simulation and Run it); examine spatial summation by firing synapses in different compartments together.
Test-cell 6
This neuron definition file contains a small 5 passive membrane compartment model that is used in to demonstrate synaptic currents. The model and the demonstrations in ‘Test-cell 6 Demo 1’ are based on Fig. 2 of Perkel, D.H., Mulloney, B., and Budelli, R.W.: Quantitative methods for predicting neuronal behavior. Neuroscience 4 (1981) 823-837.
If you have Open Simulation the ‘Test-cell 6 Demo 1’ the ‘Test-cell 6’ neuron definition file is already in memory, select the corresponding menu item at the bottom of the Neuron menu, otherwise use the Open Neuron command. A neuron definition dialog window is made. Each compartment has one synapse: #1 to #4 are excitatory (‘Fast EPSP’ and ‘Slow EPSP’), #5 is inhibitory (‘Slow IPSP’). Select the Synaptic Currents command (Neuron menu) to look at the synaptic currents subdefinitions (Fig V/48). Only one subdefinition is shown, use the
Synapse subdefinition popup menu at the top left to see another subdefinition and the Plot time course button to see a fast graphic display of the synaptic conductance, press Cancel
when done.
Suggested exercises: change the time constants of a synaptic conductance (Synaptic Currents command, select the Slow I P S P Synapse subdefinition, press Plot time course, change the close time constant to 1.2, press Plot time course, press OK, do New Simu-
lation (with Compile from Test-cell 6 1 for New simulation database) and Run it);
add voltage dependent ionic currents and see whether a spike is triggered after an EPSP (Go to
Compartment #1, (the ‘Test-cell 2’ file must be in memory), do Ionic Currents and select
the Connor Stevens Currs (if not shown), press Duplicate and OK, select the Copy of
Connor Stevens Currs in the ion currents popup menu of the compartment definition
window of Test-cell 6,do New Simulation (with Compile from Test-cell 6 1 for N e w
simulation database) and Run it). Test 7 Network Demo
This simulation run file shows reciprocal inhibition between 2 neurons in a small network (Fig VI/5). The difference in firing frequency is controlled by current injection (Current Clamp).
Open Simulation ‘Test 7 Network Demo’ (this is possible only if the previous simulation has
finished Running or is Closed) and Run it. Do New Simulation and examine the Config-
ure Plots and Current Clamp dialog windows; remark the use of the neuron definition
Test 7 Network
This network definition file models an extremely simple network of 2 small neurons.
If you have Open Simulation the ‘Test 7 Network Demo’ the ‘Test 7 Network’ network definition file is already in memory, select the corresponding menu item at the bottom of the
Network menu, otherwise use the Open Network command in the File menu to open ‘Test
7 Network’. The network definition dialog window (Fig. V/30) is shown.
-60 -40 -20 0 20 1.25 2.50 3.75 5.00 sec mV -60 -40 -20 0 20 1.25 2.50 3.75 5.00 sec mV
Fig. VI/5: the plot output of the ‘Test 7 Network Demo’ simulation after a complete
Run.
Examine the synaptic connections between the 2 neurons with the Synaptic Connections command in the Network menu (Fig. V/32). Use the Connections from popup menu to look at the connections from the Left cell and from the Right cell.
Suggested exercises: change the (axonal) delay between the 2 neurons (Synaptic Connec-
tions command, change the Delay from the Left cell to Right cell to 50 ms, press OK, do N e w Simulation (with Compile from Test 7 Network for N e w simulation data- base) and Run it); add a third neuron to the network (select the network definition window,
type ‘Middle cell’ for Local name in the third row and select Test-cell 7 in the neuron
definition popup menu, use the Synaptic Connections command to connect both the Left cell and Right cell to the Middle cell by changing the Neuron popup menu in the second
row from None to Middle cell and press OK, do New Simulation and Run it).
Test-cell 7
This neuron definition file is similar to the ‘Test-cell 2’ model, with a synapse added to the compartment #4 dendrite and a transmitter release site to the compartment #5 dendrite.
Use the Transmitter Release and Synaptic Currents commands in the Neuron menu to examine the equations used, both the dialog windows are very similar.
Test-cell 1 Clamp
This simulation data file illustrates the use of voltage clamps. It reproduces the experiment that shows the existence of an A-current: a long hyperpolarization followed by a small depolarization (as in Fig. 1B of Connor JA and Stevens CF: Voltage clamp studies of a transient outward membrane current in gastropod neural somata. J. Physiol. (London), 213 (1971) 21-30.).
-90 -80 -70 -60 -50 -40 500 1000 1500 2000 ms mV 0 20 40 60 80 100 500 1000 1500 2000 ms nA 0.0 0.2 0.4 0.6 0.8 500 1000 1500 2000 ms U
Fig. VI/6: the plot output of the ‘Test-cell 1 Clamp’ simulation after a complete Run.
The upper axis shows the membrane voltage in the unique compartment, the middle axis the clamping current and the lower axis activation and inactivation factors for the A-current (‘CS A Current’). The mechanism of A-current activation is demonstrated: a long hyperpolarization slowly removes inactivation, depolarization instantly raises the activation factor.
Use the Voltage Clamp command Configure Plots in the Simulation menu to examine how this simulation has been constructed.
Test-cell 1
This neuron definition file contains the model that Connor and Stevens used to simulate the ion currents in an Anisidoris neuron (Connor JA and Stevens CF: Prediction of repetitive firing behaviour from voltage clamp data on isolated neurone soma. J. Physiol. (London), 213 (1971) 31-53.). It is extremely simple: one excitable compartment, therefore it is only useful for ion current simulations. The ion conductance equations are contained in the 3 ‘CS…Current’
conductance definition files.
Test-cell 3
This neuron model was used to test the accuracy of the Nodus integration methods. The 27 compartment model (with many weight factors) is equivalent to a linear cable model of a spinal
α-motoneuron for which the analytical results are known (Rall, W: Branching dendritic trees and motoneuron membrane resistivity. Exp. Neurol., 1 (1959) 491-527; Segev, I, Fleshman, JW, Miller, JP and Bunow, B: Modeling the electrical behavior of anatomically complex neu- rons using a network analysis program: passive membrane. Biol. Cybern., 53 (1985) 27-40.).
The input resistance (RN) of the model was measured with a hyperpolarizing current injection, the time constant (τm) and electrical length (L) were calculated from exponential peeling data (Nodus 2).
Integration method RN τ
m L
MΩ % Err ms % Err %Err
Analytical 1.57 7.00 1.46
Hybrid Euler, ∆V=0.1 mV 1.51 -4 7.53 +8 1.58 +8 Fehlberg, Rel. Err=10-4 1.51 -4 7.09 +1 1.51 +3 Fehlberg, Rel. Err=10-8 1.51 -4 6.98 +0 1.52 +3
The results of this accuracy evaluation compare favorably with other compartmental simulation programs (Segev et al, 1985).
Test-cell 4a and 4b
‘Test-cell 4a’ and ‘Test-cell 4b’ are two different models of the same (extremely simple) neuron. ‘Test-cell 4a’ uses only node connections, while in ‘Test-cell 4b’ compartments have been fused and some compartments have branch connections (8 compartments instead of 13).
These models were used to check the accuracy of branching versus node connections. A -1.0 nA, 1000 ms current was injected in the soma (compartment #1, Nodus 2, double precision Fehlberg method, relative error was 10-8):
Model ∆V (mV) in compartment #
1 4 5 8-10/7
4a -45.62 -44.38 -43.99 -43.23 4b -45.71 -44.25 -43.86 -42.85 Error (%) -0.20 +0.29 +0.30 +0.88
The errors caused by the use of branch connections are minimal, both in the soma and in the branch compartments! A -0.5 nA, 1000 ms current was injected in a branch (compartment #5, Nodus 2, double precision Fehlberg method, relative error is 10-8):
Model ∆V (mV) in compartment #
1 4 5 8-10/7
4a -21.99 -25.17 -44.67 -22.42 4b -21.93 -26.99 -46.47 22.34 Error (%) +0.27 -7.23 -4.03 +0.36
There is a significant error in all compartments of the side-branch in which current was injected, but in the other compartments, including the soma, the error is minimal. This example shows that a branch connection is sufficiently equivalent to a node connection at the center of the (split) parent compartment for most experiments.
Test-cell 5a, 5b and 5c
‘Test-cell 5a’, ‘Test-cell 5b’ and ‘Test-cell 5c’ are neuron definition files containing three different models of the same example neuron: 5a is the original model and 5b and 5c correspond to the two reduction steps described in the ‘Nodus Implementation of Compartmental Models’ section in chapter III, Fig III/6.
The loss of accuracy caused by the model reduction was estimated by a -0.5 nA, 400 ms current in the soma (compartment #1, Nodus 2, double precision Fehlberg method, relative error 10-8):
Model ∆V (mV) in compartment # 1 6 8/7/7 18/13/10 5a -19.30 -19.01 -18.95 -18.90 5b -19.30 -19.01 -18.93 -18.88 Error (%) +0.00 +0.00 +0.11 +0.12 5c -19.45 -19.16 -19.08 -18.98 Error (%) +0.78 +0.80 +0.71 +0.45
The errors for current injections in the soma caused by the reduction are reasonably small in all compartments, including the soma.
A -0.2 nA, 400 ms current was injected in a branch (a: compartment #16,17 and 18/b: #11, 12 and 13/c:#10, Nodus 2, double precision Fehlberg method, relative error was 10-8).
Model ∆V (mV) in compartment # 1 6 8/7/7 18/13/10 5a -22.69 -22.97 -23.70 -25.55 5b -22.65 -22.94 -23.86 -26.12 Error (%) +0.14 +0.14 -0.64 -2.24 5c -22.78 -23.07 -23.99 -29.87 Error (%) +0.42 +0.42 +1.21 +16.95
The errors for current injections in the branches caused by the reduction are reasonably small in the soma, but totally unacceptable at the reduced side-branches!