Tutorial:Simulation

From QuB

Jump to: navigation, search
Prev: Single Channel Simulation Outline Next: Single Channel Measurements


The following tutorials will lead you through various simulations useful in single-channel analysis. The data files we create will be used in the analysis tutorials.

Contents

Simple

Simulating 10 segments of data at equilibrium:

  1. Build the model at right
  2. Set the entry/start probabilities to equilibrium
    • Right-click the background of the model
    • Choose Equilibrium P -> Calculate and assign
  3. Save the model (File -> Save model as) "basic model.qmf"
  4. Right-click "Sim", on the right under "Simulation", for simulation properties
  5. Set "Segment count":10, "Segment size":100000
  6. Choose "New data file"
  7. Click "Simulate"
  8. The New Data dialog appears:
    • File format: QDF (qub's native data format)
    • A/D Channels: 1 (1 signal line for the simulated current)
    • Sampling (kHz): 20
    • Scaling: 320 (why?)
  9. Click OK
  10. Save the data (File -> Save data as) "basic model sim.qdf"

Ligand-dependent

Simulating a ligand-dependent model at different concentrations:

  1. Start with the basic model above
  2. Make the opening rates ligand-dependent
    • Double-click the number 100 to open the rate properties dialog
    • Check "P" and verify the name "Ligand" is to the right of P
    • Click the number 10000
    • Check "P" and verify the name "Ligand" is the same
    • Click OK
  3. Force the simulation to start in state 1
    • Right-click state 1
    • Choose "Make start state"
  4. Save the model (File -> Save model as) "ligand-dependent.qmf"
  5. Right-click Sim for simulation properties:
    • Choose "New data file"
    • Set ligand concentration to 0.1:
      • Click the "Model" tab
      • Under "Parameters" find the cell for "Ligand" "Value"
      • Enter 0.1
  6. Click "Simulate"
  7. Fill out the New Data dialog as above
  8. Save the data (File -> Save data as) "ligand-dependent 0.1.qdf"
  9. Re-simulate with ligand concentration of 1.0:
    • Right-click Sim
    • New data file
    • Model:Parameters:Ligand value 1.0
    • Simulate
  10. Save the data as "ligand-dependent 1.0.qdf"
  11. Re-simulate with ligand concentration of 3.0
  12. Save the data as "ligand-dependent 3.0.qdf"

Pulses of Agonist

Note: the following procedure has been superseded by Simulation:DoseResponse.

We will simulate the response of the above model to pulses of agonist. If you haven't done so, create ligand-dependent.qmf. First, we create the pulse in the Acquisition Protocol window:

  1. Open the Acquisition Protocol window (View -> Acquisition Protocol)
  2. Create a new protocol file (click the document icon in the upper-left of the Acq.Proto window)
  3. Verify there's 1 D/A Channel (one stimulus variable)
  4. drag-and-drop the Step shape from the top palette to the blank grey in the middle
    Image:Step.png
  5. Configure the Step at left:
    • preDuration:0.25, preAmp: 0.0 -- it will start with 0.25 seconds of 0.0 concentration
    • Duration:0.5, Amp: 0.1 -- it will rise to 0.1 concentration for 0.5 seconds
    • postDuration:0.25, postAmp: 0.0 -- it will end with 0.25 seconds of 0.0 concentration
    • Amp incr: 0.1 -- with every repetition Amp will be increased by 0.1 (so the second rep will have Amp of 0.2)
  6. Configure the repeats:
    • Below the picture, set "Repeat stage" to 10 times
  7. Save the protocol (the third icon in the upper-left of the Acq.Proto window) as "ligand steps.qpf"

Then we simulate:
If you have QuB 1.4.0.67 or newer:

  1. Right-click Stim (StimSim)
  2. For "Stimulus file" choose "ligand steps.qpf"
  3. Under Parameters, make sure "Ligand" is assigned to "Channel" 1
  4. Check "New file" and enter an appropriate Sampling rate (e.g. 10 kHz)
  5. Click "OK"
  6. Save the data as "ligand steps.qdf"

If you have QuB 1.4.0.66 or older:

  1. Right-click Sim
  2. Choose "New data file"
  3. Click the "Simulation" tab
  4. Choose Stimulation: File
  5. Choose Stimulation File: steps.qpf
  6. Click the "Model" tab
  7. Under Parameters, set Ligand Channel to 1 (the Value disappears because it will vary)
    • Stimulus channels are numbered starting with 1 (the current is in channel 0)
  8. Click Simulate
  9. Give the new data file an A/D Channel Count of 2: one for the current, one for the stimulus
  10. Click OK
  11. Save the data as "ligand steps.qdf"

Heterogeneous

Real-life recordings often have more than one kind of channel. We will simulate a patch containing two channels: one with high open probability (Po) and one with low Po.

High Po.qmf
High Po.qmf
Low Po.qmf
Low Po.qmf
  1. Build and save the two models to the right. Set state 3 as the start state in both. Keep both open.
  2. Right-click Sim
  3. In the "Model" tab, hold down the Control key and select both models
  4. Click Simulate
  5. Save the data as "heterogeneous.qdf"

You should see clusters which are mainly closed, clusters which are mainly open, and mixed clusters which rise to a double-open level.


LiveSim

To see the effect of changes to the model, you can "LiveSim": have qub re-simulate after every change to the model. For responsiveness, use LiveSim only with small simulations.

  1. Set up a model (e.g. basic model)
  2. Right-click Sim:
    • Segment count: 1
    • Segment size: 10000
  3. Click Simulate
  4. Click "LiveSim" next to "Sim" to turn on live simulation
  5. Make some changes to the model
    • try pointing at a rate and spinning the scroll wheel
  6. When you're done, turn off live simulation by clicking "LiveSim"


Prev: Single Channel Simulation Outline Next: Single Channel Measurements
Retrieved from "http://www.qub.buffalo.edu/wiki/index.php/Tutorial:Simulation"
Personal tools