PSICS - the Parallel Stochastic Ion Channel Simulator

Stimulation and Recording

The behavior of the model can be modified by attaching voltage clamps or current clamps to particular points, and can be probed with voltage recorders to examine the membrane potential. The command signal for a clamp can be specified in two ways: either components of the profile (steps, pulses, noise) can be embedded inside the clamp definition directly; or the clamp can refer to a profile by its id. If the same profile is used in different contexts, the second approach makes models more concise and avoids unnecessary duplication.

A third clamp type, the conductance clamp, is also available. By analogy with voltage and current clamps, this has a fixed driving potential but a variable conductance. It is the closest in behavior to a normal synaptic input, and makes it easier to achieve a stable stimulation across a range of parameter values than with a current clamp. The difference is that whereas a current clamp forces a certain current into the cell, irrespective of how depolarized it becomes, the conductance clamp lets the current flow towards a fixed reversal potential and therefore will not induce extreme depolaraizations. It can also be used to simulate shunting effects of areas of membrane that are not explicitly included in the model.

Although the three clamp types share a lot of the same properties, they have different dimensions and are represented by different objects. Each profile type also appears in three flavors, giving rise to a lot of objects. However, they are structurally very similar, so familiarity with one type should reliably map to the others.

Clamp attributes

The main attributes of a clamp are the at attribute which defines where it is attached to the cell. The value should be the id of a point on the morphology. The hold attribute sets the baseline value, and either embedded profile components or a profile referred to with the profile attribute sets the command profile. In the absence of a profile, the hold value applies throughout the run, as with a steady current injection or a fixed voltage clamp. Voltage recorders share the at attribute with exactly the same meaning. Indeed, internally there is no difference between a current clamp with hold="0" and a voltage recorder.

Clamps and recorders also have three optional attributes: lineStyle, lineWidth, and lineColor. These are suggestions as to how the results should be rendered and are stored in the output files for use by plotting applications.

Profiles

A profile simply has an id, a start value in the appropriate units and then zero or more embedded elements of type xxxPulse, xxxStep, or xxxNoise. A step is a transition from the current value to a new value which stays there, whereas a pulse is a step to a new value which is held for a certain time and then reverts to the original. The noise profile provides a simple autoregressive moving average, AR(1), noise model where the value W_t at time t is simply given by W_t = a W_t-1 + (1 - a) X where X is a Gaussian random variable. If a is small, then the noise has mostly high frequencies. If a is close to 1, the signal stays closer to its previous value and has more energy at low frequencies. The parameters do not give direct control over a and the variance of X but rather set the overall properties of the profile (mean value, amplitude, and timescale) from which they are computed.

The step and pulse elements have an optional repeatAfter attribute that can be used to define repeating sequences. It gives the time from the beginning (not the end) of the pulse after which it should be reapplied, so it is just the reciprocal of the frequency.