Voltage/Current Clamp Plots
Protocols
The dropdown contains the list of protocols to which the model was subjected. Select one from the drop down to see the model's response.
Stimuli
Some protocols have multiple stimuli (e.g. voltage levels held or current amplitudes injected). If so, a "Stimulus" slider will be visible when a protocol with multiple stimuli is selected.
When visible, drag the slider left/right to see the model's
response to a specific protocol stimulus. By default, the traces of all protocol stimuli are shown superimposed, each trace indicated by a different color.
Meta-Protocols
Some models will have additional meta-protocol parameters (e.g. different calcium concentration levels, random noise seeds). If available, use the second slider to see the
effect of changing the meta-protocol parameter on the model response. When both sliders are visible, their values can be changed independently.
Trace detail
Using the mouse, hover near a point on a trace to see a popup with the point details. Top value shows the time. The bottom left value shows the name of the protocol stimulus,
and the bottom right value shows the value of the plotted variable (e.g. voltage or current)
Zoom
The plots can be zoomed in/out to see plot details. On the right side of the plot, use the [+] and [-] buttons to zoom in/out on the center of the plot.
Pan
Once zoomed, the plots can be panned by dragging the mouse or swiping fingers sideways.
Reset Plot
Once a zoom/pan position is set, it will be maintained when the stimulus/meta-protocol parameter is changed. To reset the zoom/pan,
click the circular arrow button below the zoom out button. Plot zoom will also be reset when the protocol is changed.
State Equations
The total number of state variables used in this model, as reported by NEURON.
Optimal Time-Step
Summary
The fixed time-step that provides the best tradeoff between model error and run time.
Details
Models were subjected to a benchmark current injection protocol (see Electrophysiology tab, Time Step Sensitivity protocol) using
various fixed time step sizes.
The resulting membrane potential was compared, at 1 ms intervals, to the membrane potential obtained using
the smallest time step (1/1024 ms). For each time-step size, mean percent error difference and run time were measured.
The error and run time were normalized and their sums computed for each time step size. The time-step size where the sum was the lowest
was chosen as the optimal time-step.
Optimal Time-Step Benchmark Run Time
This model's runtime using its optimal time-step as a fraction of Hodgkin-Huxley model's run time using its optimal time-step.
For example, 50 HH would mean that this model ran 50 times slower than the Hodgkin-Huxley model. While, 0.25 HH would mean the model ran 4 times faster.
Sections
The total number of NEURON sections used in this model.
Compartments
The total number of compartments used in this model, as reported by NEURON.
Optimal Time-Step Error
The percent error, relative to the smallest fixed time-step, that results when using the optimal time-step.
Maximum Stable Time-Step
The largest time-step (up to 1.0 ms) that did not result in numerical instabilities during the current injection benchmark protocol.
Maximum Stable Time-Step Error
The percent error, relative to the smallest fixed time-step, that results when using the maximum stable time-step.
Max. Stable Time-Step Benchmark Run Time
This model's runtime using its maximum stable time-step as a fraction of Hodgkin-Huxley model's run time using its maximum stable time-step.
CVODE Steady State Step Frequency
The number of steps required to compute 1 sec of non-spiking model activity using NEURON's variable step CVODE integration method.
CVODE Steps Per AP
The mean number of additional steps required to compute one action potential using NEURON's variable step CVODE integration method.
CVODE Benchmark Run Time
This model's runtime to compute 10 action potentials per second using variable time-step method as a fraction of Hodgkin-Huxley model's run time.
Electrophysiology Type
The closest cell electrophysiology cluster.
Differentiating Features
The electrophysiology properties which distinguish this cell model cluster from other models.
Models with Similar Electrophysiology Properties
The list of cell models that have similar values of electrophysiology properties. The models further down the list are less similar than those near the top.
Is Passive
Whether this cell model contains only a passive/leak channel.
Is Intrinsically Spiking
Whether this cell model produces spikes without stimulaion.
Resting Voltage
The resting voltage of this cell model.
Rheobase Current Interval
The upper point of the interval is the lowest square current amplitude of 1 sec long that produces 1 or more spikes. The lower point is the largest current that does not result in spikes.
Threshold Current Interval
The upper point of the interval is the lowest square current amplitude of 3 ms long that produces 1 or more spikes. The lower point is the largest current that does not result in spikes.
Bias Current
The amplitude of a square current 1 sec long that results in the specified steady state voltage.
Testing Temperature
The temperature at which the simulations were performed.
Stability Interval
The minimum and maximum 3 ms square voltages (for channels) or currents (for cells) that this model could tolerate as inputs without resulting in numerical instabilities ("blow-ups").
AP 1-2 Amplitude Drop
Difference in the voltage value between the amplitude of the first and second AP.
AP 1 Steady State Amplitude Change
Steady state AP amplitude is calculated as the mean amplitude of the set of APs
that occurred during the latter third of the current step.
AP 1 Amplitude
Amplitude of the first AP.
AP 1 Width at Half Height
Amount of time in between the first crossing (in the upwards direction) of the
half-height voltage value and the second crossing (in the downwards direction) of
this value, for the first AP. Half-height voltage is the voltage at the beginning of
the AP plus half the AP amplitude.
AP 1 Width (Peak To Trough)
Amount of time between the peak of the first AP and the trough, i.e., the minimum of the AHP
AP 1 Rate of Change Peak to Trough
Difference in voltage value between peak and trough over the amount of time in between the peak and trough.
AP 1 AHP Depth
Difference between the minimum of voltage at the trough and the voltage value at
the beginning of the AP.
AP 2 Amplitude
Amplitude of the second AP.
AP 2 Width at Half Height
Same as "AP 1 Width at Half Height" but for second AP.
AP 2 Width (Peak to Trough)
Same as "AP 1 Width (Peak to Trough)" but for second AP.
AP 2 Rate of Change Peak to Trough
Same as "AP 1 Rate of Change Peak to Trough" but for second AP.
AP 2 AHP Depth
Same as "AP 1 AHP Depth" but for second AP.
AP 1-2 Amplitude Change Percent
Difference in AP amplitude between first and second AP divided by the first AP
amplitude.
AP 1-2 Half Width Change Percent
Difference in AP width at half-height between first and second AP divided by the
first AP width at half-height.
AP 1-2 Rate of Change Peak to Trough Percent Change
Difference in peak to trough rate of change between first and second AP divided
by the first AP peak to trough rate of change.
AP 1-2 AHP Depth Percent Change
Difference in depth of fast AHP between first and second AP divided by the first
AP depth of fast AHP.
AP 1 Delay Mean
Mean of the delay to beginning of first AP over experimental repetitions of step
currents.
AP 1 Delay SD
Standard deviation of the delay to beginning of first AP over experimental
repetitions of step currents.
AP 2 Delay Mean
Same as "AP 1 Delay Mean" but for second AP.
AP 2 Delay SD
Same as "AP 1 Delay SD" but for second AP.
Burst 1 ISI Mean
Initial burst interval is defined as the average of the first two ISIs, i.e., the average
of the time differences between the first and second AP and the second and third
AP. This feature is the average the initial burst interval across experimental
repetitions.
Burst 1 ISI SD
The standard deviation of the initial burst interval across experimental repetitions.
Initial Accommodation Mean
Initial accommodation is defined as the percent difference between the spiking rate of the
*first* fifth of the step current and the *third* fifth of the step current.
Steady State Accommodation Mean
Steady-state accommodation is defined as the percent difference between the spiking rate
of the *first* fifth of the step current and the *last* fifth of the step current.
Accommodation Rate to Steady State
The percent difference between the spiking rate of the *first* fifth of the step current and
*final* fifth of the step current divided by the time taken to first reach the rate of
steady state accommodation.
Accommodation at Steady State Mean
Accommodation analysis based on a fit of the ISIs to an exponential function:
ISI = A+B*exp(-t/tau). This feature gives the relative size of the constant term (A) to
the term before the exponent (B).
Accommodation Rate Mean at Steady State
Accommodation analysis based on a fit of the ISIs to an exponential function.
This feature is the time constant (tau) of the exponent.
ISI CV
Coefficient of variation (mean divided by standard deviation) of the distribution
of ISIs.
ISI Burst Mean Change
Difference between the first and second ISI divided by the value of the first ISI.
Spike Rate (Strong Stimulation)
Firing rate of strong stimulus.
AP 1 Delay Mean (Strong Stimulation)
Same as "AP 1 Delay Mean" but under strong stimulation.
AP 1 Delay SD (Strong Stimulation)
Same as "AP 1 Delay SD" but under strong stimulation.
AP 2 Delay Mean (Strong Stimulation)
Same as "AP 2 Delay Mean" but under strong stimulation.
AP 2 Delay SD (Strong Stimulation)
Same as "AP 2 Delay SD" but under strong stimulation.
Burst 1 ISI Mean (Strong Stimulation)
Same as "Burst 1 ISI Mean" but under strong stimulation.
Burst 1 ISI SD (Strong Stimulation)
Same as "Burst 1 ISI SD" but under strong stimulation.
Ramp First Spike Time
The delay to first AP after the onset of 1 rheobase/sec ramp current.
Frequency Filter Type
The type of input frequency filter of this cell in response to square current tripplet stimulation.
Either Constant (no filter), Low-Pass, High-Pass, Band-Pass, or Band-Stop.
Frequency Filter Pass Above
The input frequency above which this cell has an increased spiking response.
Frequency Filter Pass Below
The input frequency below which this cell has an increased spiking response.
