Model
From QuB
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The Model window is used to display and edit kinetic models. The right-hand panel lists open model files. The left-hand panel shows the current (active) model.
Contents |
Current Model
The elements of a model are described in Model Theory. They are visually represented as in the following example:
States
- A, B
- A state is represented by a numbered, colored box.
- States are numbered automatically in the order they're created. To change the numbering, "Set index" in the #State Menu.
- A state's entry probability -- the chance a recording will start in that state -- is often abbreviated "starting prob", "Pr" or "pr0"
- To add a state, click anywhere in the background.
- To move a state, drag it.
- To see info about a state and its class, point the mouse at it. Show tips must be enabled.
State Menu
Right-click a state for the following menu:
- Make start state
- sets this state's Pr0 to 1.0, and all others to 0.0
- Set index
- prompts you to give this state a new number
- Delete state
- deletes this state
- Grab
- sets the mean amplitude and standard deviation of this state's Class, from the selected Data
- Properties
- shows the State Properties dialog, where you can edit Pr0, Class (color), and class amplitude and std.dev
Classes
- C
- All states of the same color share the same amplitude and std. deviation. They are indistinguishable by amplitude. Class 1, black, is for "closed" states. A simple model will have only black (closed) and red (open) states.
- To change a state's color, double-click or shift-double-click, or use State Properties.
- To change a class's amplitude and standard deviation, use State Properties on any state of that color. You can also Grab those values from the selected Data, or Grab all ...
- To show info about a class, point the mouse at any state of that color. Show tips must be enabled.
Rates
- D, E
- Two states are connected if a direct transition is possible. The rate constants are written on the arrow. D is labeled with "p" to indicate pre-exponential (concentration) dependence.
- To connect two states, right-click and drag from one to the other.
- To remove a connection, right-click it and choose "Delete connection"
- To edit a rate constant, double-click it to show Rate Properties, or click once and spin the scroll wheel. Holding down control or shift increases or decreases the scrolling speed.
- To show info about a connection, point the mouse at a rate constant. Show tips must be enabled.
Channel Count
- F
- the number of ion channels in the patch
- you can also edit this number in Model Properties.
Background
- G
- To see a tool-tip with information about the whole model, point the mouse at the background near the top of the window. Show tips must be enabled.
Right-click Menu
Right-click in the background for the following menu:
- Equilibrium P
- Calculate
- prints several statistics in the Report window, including
- Q Matrix
- A Matrix (A = eQΔt)
- equilibrium probability
- eigenvalues of Q
- predicted macroscopic current
- These stats and more are available in the Model Report
- Calculate and assign
- prints the stats, as above, and sets each state's entry probability to the equilibrium probability
- Advance P
- changes each state's entry probability by multiplying by the A matrix. This is like running the model for Δt
- Enforce constraints
- modifies rates as necessary to satisfy loop-balance and other kinetic constraints
- Randomize rates
- This function calculates the free parameters corresponding to the current rates, and perturbs them by SE (a gaussian with Avg = freepar, Std = freepar*SE)
- Energy landscape
- Displays the model as energy wells and barriers. If your model has a stimulus dependence, you can see the effect of different stimuli using a slider.
- Use global conditions
- toggles between using stimulus values from the Data, or from the Edit Global Conditions dialog. This may be useful in combination with "Equilibrium P" -> "Calculate and assign"
- Edit global conditions
- shows the Edit Global Conditions dialog
- Un-Merge Models
- (for models created by Modeling:Model Merge)
- copies the (possibly modified) rate constants back into the source models
- Cut, Copy, Paste
- standard clipboard operations on the entire model
- Grab all amps increasing/decreasing
- Calculates the amplitude and std deviation of all Classes, using the Modeling:Amps algorithm on selected Data. Use "increasing" if your data has open_amp > closed_amp. Double-check the class amplitudes -- if they're not reasonable, Grab or manually edit one class at a time.
- Sends the model image to the printer. You are prompted with options
- Copy Image
- Copies the model image to the clipboard. You are prompted with options
- Properties
- Shows the Model Properties dialog, where you can edit display settings, rate constants, and constraints.
Files
The right-hand panel lists all open model files. Use the File menu to open, save and close model files. To edit the active model's Properties, double-click its entry. Right-click an entry for the following menu:
Files Menu
- Close
- closes the model file, prompts you to save any changes
- Revert to saved
- undoes all changes since the model was last saved
- Show tips
- toggles the display of tool-tips when you point at elements in the model
- Edit global conditions
- shows the Edit Global Conditions dialog
- Properties
- shows the Model Properties dialog for the active model
See Also
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