Simulation:Simulate
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Simulation generates microscopic and macroscopic currents from a markov model. Currents can be stimulated, with ligand- and voltage- dependent rates, and voltage-dependent conductance. Various noise and artifacts can be added for verisimilitude.
Contents |
Properties
Data
| Segment count | Number of data segments to simulate. Each segment starts with entry probabilities from the model |
|---|---|
| Segment size | number of samples in each data segment |
| Idealized data | whether to overlay the ideal (sampled) event durations |
| Output | state: the "class" of each event is actually the state number class: (normal style) |
| Randomize | Use a different random seed each time |
| Seed | Same seed, same model, same options should yield the same data. Ignored if Randomize is checked |
| Rec transitions | |
| New data file | You will be prompted to create a new file when you Simulate |
| Replace data | Previous simulated data will be cleared and new data simulated in its place. Technically, it will use the file last simulated with this model, or if none, the file last simulated with any model. |
| Append data | Data will be written at the end of the last file simulated (same technicality) |
| Append data to current file | Data will be written at the end of the current data file |
Model
Pick a model (by default the current one) and set channel count to the number of independent ion channels in the simulated patch. Ctrl-click to select more than one model -- their simulations will be added together.
Set the Value of any parameters which are used in the model(s). For simulations with a changing stimulus, assign each changing stimulus to a Channel, starting with 1. Use Presets to load/save the entire contents of Parameters.
Simulation
| Stimulation | None: Hold all experimental parameters constant at their Value File: Vary experimental parameter(s) according to a protocol or data file<br Script: Vary experimental parameter(s) according to a KPL script |
|---|---|
| Stimulation file | Choose from all open Acquisition Protocol or Data files. The file should have as many A/D channels as the model has experimental variables. Assign them (beginning with number 1) in the Model tab |
| Stimulation script | written in KPL |
| Response | Stochastic: Sum the random current from each of channel count channels Deterministic: Scale the predicted macroscopic current by channel count |
| i=g*(V - Vrev) | Check this option if you want to simulate current responses scaled with the voltage |
| V[mV] | The voltage is either this value, or taken from the stimulation, if any |
| I leak | Check this option if you want to add a "leak" current, also scaled with voltage. It simulates, e.g., a recording from a neuron |
| Glk [nS] | The conductance of Ileak |
| Vlk [mV] | The reversal voltage for Ileak |
Staircase
| Staircase | |
|---|---|
| Step size(s) | |
| Step std | |
| No Jump Class |
Baseline
The following artifacts can be added to the simulated current:
| Random fluctuations | |
|---|---|
| Deterministic periodic component | sine wave |
| Linear Gaussian model | each baseline point deviates a little from the previous point |
| Random jumps and exp recovery | |
| Deterministic linear drift |
Movie
See Also
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