NeuroML Database

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.

Input Resistance

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

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 Median

Median 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.

Documentation

Overview Video: Keyword and Ontology-Assisted Search

Watch the above video to get a quick overview of the main features of the search engine: keyword search and ontology-assisted search which allows searching for models by brain region and neurotransmitter. Once located, the NeuroML code of a model can be downloaded as a single file.

Keyword Search

Keyword search is, as its name implies, a simple search for computational models by keywords. Models whose model name, author, publication title, or description contains any of the search terms will be returned in the results. The results for keyword search are shown on the left.

Ontology Search

The ontology-assisted search, showing results on the right, does not match the entered terms, but instead matches models that are related to one or more of the entered terms. Specifically, when a brain region (i.e. hippocampus) is entered as a term, all models within that region will be returned. When a neurotransmitter is entered (i.e. GABA), models of cells releasing it will be shown. Furthermore, cells with specific neurotransmitter within specific regions can be found by entering a neurotransmitter and a region as the search terms (i.e. "GABA cerebellum" will return all GABA releasing cells located in the cerebellum).

Limitations

The search engine currently supports only the Located_in, Is_part_of, and Neurotransmitter relationships. Furthermore, only models of at most one relationship (edge) away will be returned.