Natalie Williams Week 14: Difference between revisions

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(→‎April 23, 2015: New section as well as description of edits needed to make to wkbk for GRNSight)
(→‎Running the GRNmodel on MATLAB: Added new section as well as questions that will help interpret the data)
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To visualize the first run where the parameters and production rates were optimized and "guessed", the out_network_weights sheet had to be deleted from the workbook. I then renamed the out_network_optimized_weights to network_optimized_weights. When that was uploaded to GRNSight, the colors as well as the thickness of the lines were seen.
To visualize the first run where the parameters and production rates were optimized and "guessed", the out_network_weights sheet had to be deleted from the workbook. I then renamed the out_network_optimized_weights to network_optimized_weights. When that was uploaded to GRNSight, the colors as well as the thickness of the lines were seen.


==Analyzing the Results of the GRNmodel==
===Graphs===
Examine the graphs that were output by each of the runs. Which genes in the model have the closest fit between the model data and actual data? Why do you think that is? How does this help you to interpret the microarray data?


===Between Strains===
Which genes showed the largest dynamics over the timecourse? Which genes showed differences in dynamics between the wild type and the other strain your group is using? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?
===Frequencies, Weights, and Production Rates===
Examine the bar charts comparing the weights and production rates between the two runs. Were there any major differences between the two runs? Why do you think that was? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?


{{Template:Natalie Williams}}
{{Template:Natalie Williams}}

Revision as of 12:19, 27 April 2015

Running the GRNmodel on MATLAB

April 22, 2015

I ran a version of the model before coming to class. To view the outputs and figures, download the following link:
Scer vs. Spar

April 23, 2015

In class:
This file output was incorrect due to the optimization parameters. iestimate was set to 0, when it should have been equal to 1. The alpha input was also set to 1.00E-10 when it should have been equal to 0.01.
These changes were made and were rerun during class.

These are the following figures from MATLAB estimation outputs.

Out of Class

To visualize the first run where the parameters and production rates were optimized and "guessed", the out_network_weights sheet had to be deleted from the workbook. I then renamed the out_network_optimized_weights to network_optimized_weights. When that was uploaded to GRNSight, the colors as well as the thickness of the lines were seen.

Analyzing the Results of the GRNmodel

Graphs

Examine the graphs that were output by each of the runs. Which genes in the model have the closest fit between the model data and actual data? Why do you think that is? How does this help you to interpret the microarray data?

Between Strains

Which genes showed the largest dynamics over the timecourse? Which genes showed differences in dynamics between the wild type and the other strain your group is using? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?

Frequencies, Weights, and Production Rates

Examine the bar charts comparing the weights and production rates between the two runs. Were there any major differences between the two runs? Why do you think that was? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?

Back to User Page: User:Natalie Williams
To view the Course and Assignments:BIOL398-04/S15


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