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.

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.

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.

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.

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.

The closest cell electrophysiology cluster.

The electrophysiology properties which distinguish this cell model cluster from other models.

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.

Whether this cell model contains only a passive/leak channel.

Whether this cell model produces spikes without stimulaion.

The resting voltage of this cell model.

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.

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.

The amplitude of a square current 1 sec long that results in the specified steady state voltage.

The temperature at which the simulations were performed.

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").

Difference in the voltage value between the amplitude of the first and second AP.

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.

Amplitude of the first AP.

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.

Amount of time between the peak of the first AP and the trough, i.e., the minimum of the AHP

Difference in voltage value between peak and trough over the amount of time in between the peak and trough.

Difference between the minimum of voltage at the trough and the voltage value at the beginning of the AP.

Amplitude of the second AP.

Same as "AP 1 Width at Half Height" but for second AP.

Same as "AP 1 Width (Peak to Trough)" but for second AP.

Same as "AP 1 Rate of Change Peak to Trough" but for second AP.

Same as "AP 1 AHP Depth" but for second AP.

Difference in AP amplitude between first and second AP divided by the first AP amplitude.

Difference in AP width at half-height between first and second AP divided by the first AP width at half-height.

Difference in peak to trough rate of change between first and second AP divided by the first AP peak to trough rate of change.

Difference in depth of fast AHP between first and second AP divided by the first AP depth of fast AHP.

Input resistance calculated by injecting weak subthreshold hyperpolarizing and depolarizing step currents. Input resistance was taken as linear fit of current to voltage difference.

Mean of the delay to beginning of first AP over experimental repetitions of step currents.

Standard deviation of the delay to beginning of first AP over experimental repetitions of step currents.

Same as "AP 1 Delay Mean" but for second AP.

Same as "AP 1 Delay SD" but for second AP.

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.

The standard deviation of the initial burst interval across experimental repetitions.

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 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.

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 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 analysis based on a fit of the ISIs to an exponential function. This feature is the time constant (tau) of the exponent.

Coefficient of variation (mean divided by standard deviation) of the distribution of ISIs.

Median of the distribution of ISIs.

Difference between the first and second ISI divided by the value of the first ISI.

Firing rate of strong stimulus.

Same as "AP 1 Delay Mean" but under strong stimulation.

Same as "AP 1 Delay SD" but under strong stimulation.

Same as "AP 2 Delay Mean" but under strong stimulation.

Same as "AP 2 Delay SD" but under strong stimulation.

Same as "Burst 1 ISI Mean" but under strong stimulation.

Same as "Burst 1 ISI SD" but under strong stimulation.

The delay to first AP after the onset of 1 rheobase/sec ramp current.

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.

The input frequency above which this cell has an increased spiking response.

The input frequency below which this cell has an increased spiking response.