# User:Alondra Vega/Notebook/Research/2010/05/28

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## Today's Work

• To begin practicing in Matlab, we created a test_data_file.xls. In this file my job was to change the parameter values, the weights.
• Parameters 2 and 3 were to be changed simultaneously to show the greatest effect.
• Separately, parameter 6 was to be changed to show how the fourth gene would be affected.
• The network that we are working with has four genes.

### Trial 1

• To start things off, I left all parameter values both weights and thresholds equaling 1.
• All genes have an equilibrium at 1 with different graph behaviors.

### Trial 2

• For the first trial I decided to make the parameter values of 2 and 3 smaller than 1. I made them equal 0.5. The gene that showed a difference in the way that it behaved was Gene 3.
• All of the genes were at equilibrium at 1. Even though some of the parameters changed they still all went to 1.

### Trial 3

• For the second trial I decided to make both of the parameter values of 2 and 3 greater than 1. I made them equal 5.
• Gene1's equilibrium point changed. It seems that it is now approaching 1.5.
• Gene2's equilibrium also changed. It is now approaching 2. A value twice as big as the first equilibrium state.
• Gene3's equilibrium changed to 1.7.
• Gene4's equilibrium seems to be approaching a number less than 1.5.
• All genes went to a different equilibrium value.

### Trial 4

• For this trial I changed the second parameter to a number greater than 1 and the third parameter value to a number less than 1. The second parameter value will stay as 5 and the third parameter value will change back to 0.5.
• Gene1's equilibrium point seems to have shifted a little higher up from Trial 2. It seems to be arou8nd the value of 1.6.
• Gene2's equilibrium value has shifted lower than in Trial 2. It now seems to be approaching the value of 1.6 or 1.7.
• Gene3's equilibrium value has also lowered by 0.1. It is now 1.6.
• Gene4's equilibrium value did not have a lot of variance.

### Trial 5

• For Trial 4 I switched the values of Trial 3. So now the second parameter has a value of 0.5 and the third parameter has a value of 5.
• Gene1's equilibrium point had a very small variance. it may have been a 0.1 difference or less.
• Gene2's equilibrium point decreased to 1.5.
• Gene3's equilibrium point also decreased to 1.5.
• Gene4's equilibrium point had a very small variance.

### Trial 6

• For Trial 5, both parameters 2 and 3 were changed to be -1. This is to observe the behavior that a negative weight has on the model.
• Gene1's equilibrium point went back to 1, but before it went to 1 it had a small decrease in slope just below 1 and then it jumped back to 1.
• Gene2's equilibrium also went back to one having the same behavior as Gene1 did. It just had a deeper steep in the decrease in slope.
• Gene3's equilibrium also went back to 1. It went passed 1 to a little over 1.1 and then back down to about 0.82 before it went to equilibrium.
• Gene4's equilibrium behaved as gene1. It had a little variance from the rest of the changes.

### Trial 7

• For Trial 6, the second parameter was left as negative and the third parameter was changed back to positive 1.
• Gene1's equilibrium point did not change much from Trial 5.
• Gene2's equilibrium is 1, but before it got there it had a dramatic change in slope. It went down from 0.6 back up to 1.
• Gene3's equilibrium point changed the most in this trial. It went up to about 1.22 and created a peak in the graph. Then it decreased to have an equilibrium point at 1.
• Gene4's equilibrium point showed minimal variance.

### Trial 8

• For Trial 7, the second parameter was changed to 1 and the third weight value was changed to -1.
• Both Gene1 and Gene4 showed little variance.
• Gene2's model behavior was similar to the behavior it had during Trial 6, just with less of a dramatic drop below 1. Its equilibrium is still 1.
• Gene3's equilibrium point is still 1, but it went from about 1.56 to 1.

```We notice that the equilibrium point for Gene4 did not have a lot of variance, thus we will look at the weight
that affects this gene. It is weight 6.  For the following trials only the sixth parameter,weight, value
will be changed.
```

### Trial 9

• For this trial the value for parameter 6 was changed to 0.5.
• For all graphs the equilibrium value did not go to 1, but the behavior of the graphs did no change.

### Trial 10

• For this trial, I changed the parameter value from 0.5 to 5.
• Genes 1-3 did not show a lot of variance.
• Gene4's equilibrium point changed to 2. Twice as much as the original. This is the first trial that shows Gene4 changing its equilibrium value with a great difference.

### Trial 11

• For this trial I changed the sixth weight into -1 to see how it would affect Gene 4.
• Genes 1-3 still did not show a lot of variance in this trial.
• Gene4's equilibrium went back to 1. The graph did show a slight decrease in slope before approaching 1, in comparison to all the previous trials.