# BIOL398-03/S13:Class Journal Week 13

(Difference between revisions)
 Revision as of 17:35, 18 April 2013 (view source) (→James P. McDonald: grammar fix)← Previous diff Revision as of 17:42, 18 April 2013 (view source) (→James P. McDonald: added to question 3)Next diff → Line 44: Line 44: #*If you add a 0 in place of a 1 it represents the deletion of that particular gene. You can then run the experiment with this deletion to see its effect. #*If you add a 0 in place of a 1 it represents the deletion of that particular gene. You can then run the experiment with this deletion to see its effect. #Return to the chemostat. In concept, without worrying about creating matlab code, how might you use the least squares technique to get parameters from the ter Schure et al experiments? #Return to the chemostat. In concept, without worrying about creating matlab code, how might you use the least squares technique to get parameters from the ter Schure et al experiments? - #*The least squares technique relies on an approximation, therefore inputting a line of best fit into the ter Schure can allow you to approximate the parameters of the experiment. + #*The least squares technique relies on an approximation and data fitting, therefore placing a line of best fit into the ter Schure data can allow you to approximate the parameters of the experiment. #Read over the Vu and Vhoradsky paper in this week's reading list. Is the method of the paper different from that in class? If so, in what ways? #Read over the Vu and Vhoradsky paper in this week's reading list. Is the method of the paper different from that in class? If so, in what ways? #* #*

## Reflection

Kevin Matthew McKay 01:44, 17 April 2013 (EDT)

1. Look over the excel workbook input file. How might you change the network to add more genes/transcription factors?
• In the Excel spreadsheet, you can add more columns/rows to add more genes/transcription factors to run.
2. How might you run a computer experiment to examine the deletion of a gene?
• Instead of 1, you could input a value of 0 to show that there is a deletion. This change will show how the deletion affects other genes/transcription factors.
3. Return to the chemostat. In concept, without worrying about creating matlab code, how might you use the least squares technique to get parameters from the ter Schure et al experiments?
4. Read over the Vu and Vhoradsky paper in this week's reading list. Is the method of the paper different from that in class? If so, in what ways?

• How might you change the network to add more genes/transcription factors?
• How might you run a computer experiment to examine the deletion of a gene?
• Delete a gene or alter its transcription to zero to look at the effect on the other genes.
• Return to the chemostat. In concept, without worrying about creating matlab code, how might you use the least squares technique to get parameters from the ter Schure et al experiments?
• You could look a best fit line of the ter Schure data to estimate the parameters
• Read over the Vu and Vhoradsky paper in this week's reading list.Is the method of the paper different from that in class? If so, in what ways?
• Vu and Vhoradsky set limit of parameters to 500.They looked at cyclin networks.

1. Look over the excel workbook input file. How might you change the network to add more genes/transcription factors?
• More genes and transcription factors can be added to the excel file very easily. All you would have to do is add more columns and rows to the table and add the new genes and transcription factors.
2. How might you run a computer experiment to examine the deletion of a gene?
• If a gene is deleted it will have no ability to up or down regulate any other gene. The easiest way to examine the deletion of a gene is to delete it from the model.
3. Return to the chemostat. In concept, without worrying about creating matlab code, how might you use the least squares technique to get parameters from the ter Schure et al experiments?
• You would have to use the least square technique to fit a line through their data. If you are able to get the lines to be similar, then you would have an estimate of what the parameters were for their experiment.
4. Read over the Vu and Vhoradsky paper in this week's reading list. Is the method of the paper different from that in class? If so, in what ways?
• In the Vu and Vhoradsky paper they look at 40 cell cycle regulated genes. The method for calculating is not that different from the one we went over in class. In this paper the methods are being used on a greater scale. "The procedure was applied to 40 yeast cell cycle regulated target genes and 184 potential regulators" In the paper there were also comparisons between linear and non-linear modeling.

Salman Ahmad 18:13, 18 April 2013 (EDT)

## James P. McDonald

1. How might you change the network to add more genes/transcription factors?
• You can add more genes/transcription factors in the network in the excel file by adding additional rows and columns with new genes or transcription factors.
2. How might you run a computer experiment to examine the deletion of a gene?
• If you add a 0 in place of a 1 it represents the deletion of that particular gene. You can then run the experiment with this deletion to see its effect.
3. Return to the chemostat. In concept, without worrying about creating matlab code, how might you use the least squares technique to get parameters from the ter Schure et al experiments?
• The least squares technique relies on an approximation and data fitting, therefore placing a line of best fit into the ter Schure data can allow you to approximate the parameters of the experiment.
4. Read over the Vu and Vhoradsky paper in this week's reading list. Is the method of the paper different from that in class? If so, in what ways?