Tutorial:Basic Model
From QuB
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We will build a "closed-open-closed" (COC) model to review/illustrate the task of model building.
Contents |
New Model
1. Start off with a new model. Do this by selecting New Model from the File menu or selecting the Create New Model toolbar button. The New Model window, will pop-up, allowing you to: name the new model, select the file type (preferably .qmf), and select its location. Clicking the (…) button to the right of the File name window will allow you to browse for the desired file location. Click OK, and a simple 2 class; 2 state model will appear in the Model window.
Add a State
2. Add another state to the model: Left click anywhere within the model window. A new state numbered "3" should appear with the default class color (Class 1, black).
Add a Rate
3. Draw a connection between states 2 and 3: Position the mouse pointer over the 2nd state, hold down the right mouse button while dragging a line to the state 3. When over the state 3 release the mouse button and a connection line with 2 new rate constants (default value is 100) should appear.
Classify (color) States
4. Since the color scheme already denotes the two classes we wish to assign (a closed class and an open class) we do not need to change the color of any of the states. If you wish to practice class changes simply double-click the left mouse button on a state or else right-click on a state, go to the Properties window, and select a different color. Make sure when you are done you recreate a model with 3 states and 2 classes (the odd color should be state 2). If you make a mistake, you can delete a state by right clicking on it and selecting Delete state.
Add Class Amplitudes and Standard Deviations
5. Position the mouse pointer over any state and wait a second. A pop-up window appears which lists the state values: pr0 for the probability of starting in that state, amp for amplitude of the current passing through the channel at that state, and sd for standard deviation of the current. (grp is reserved for future use, and will not be discussed here.) To change these values, Right-Click on the state and select Properties: a State and class properties window appears. Do this for State 2, and make sure that the Amplitude value for the red class is "1" (For now use positive values for amplitudes). Similarly, check that the amplitude value for the black class (state 1 or 3) is "0". The default value for Standard Deviation for class 1 (black) is ".1" (this value is fine for this model). The default value for other colors is > .1 and can be changed. For this model, change the S.D. property of state 2 to "0.1," and click OK. Note that changing the properties of one state will automatically change all other states of the same class in the model.
Add initial probabilities to the model
6. The default value for the starting probability of a state is 0. If nothing is changed, or if all of the starting probabilities are zero, Sim makes it equally likely for the channel to begin in any state. If you add starting probabilities to states and the sum of all the probabilities in the model are > or < 1 QuB's algorithms will scale each starting value so that they add up to 1. For now, leave each starting probability set to 0, so that it is equally likely to begin in any of the three states.
Practice moving the model around in the Model window
7. Position the pointer over any state. Hold down the left mouse button and drag the state to anywhere in the Model window until you are comfortable with the position (the connection lines will follow). When you are comfortable with the positioning of the model, continue on.
Set rate constants
8. Position and hold the pointer over any of the rate constants. A help window pops up with the default settings for the rate constants. Set the backward rate constant between states 1 and 2 (k21) equal to 200: Double click the rate constant on the same side as the arrow pointing to state 1. The Rate properties window appears, with a picture of the model. Change k0 to "200." Now click on other rates in the picture and change them so that the final model consists of the following rates: k12 = 100, k21 = 200, k23 = 200, k32 = 10000. Finally, click OK. The effects of changing voltage, concentration, and k1 will be illustrated other tutorials.
Save model
9. The model design is now complete and it is important to save the model before using it. A good way to organize your data is to make a folder of models for each type of data. Create a directory called "Example Models" and save your new model file there. Select Save Model As under the File menu. Selecting the drive you wish to save the file on (usually the C:\ drive) does this from the Save in drop down menu. Once the contents of (C:) are listed, select the tool button for create new folder and type in the name of the new folder ("Example Models"). Double-click the new folder to make it the active directory. Type in the name of this new model under File Name (i.e., model1). An extension is not necessary; QuB will automatically add .qmf to the file name. Select Save to complete the task.
See Also
- Model Theory
- Model window
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