Bar Chart Analysis of Model Runs for 5, "15"-Gene Networks

[bklein7]

Bar charts will be used to assess modeling results generated in #265 per the guidelines specified during the Data Analysis Team meeting on Monday, November 7th:

1. Make two separate bar charts showing production_rate & threshold_b values generated for each transcription factor, clustered to show the results from all 5 networks (do not include dCIN5 results until @kdahlquist updates this network).

2. Make a bar chart showing the MSE values for each gene within the individual networks, clustered to show the different MSE values computed for each strain present within the network model.

[bklein7]

Moving forward, we will consider coding a function in MATLAB to produce these graphs as part of GRNmap. However, we will focus on producing these results in Excel for now to expedite this process.

[bklein7]

I created all requested bar charts and uploaded a PowerPoint presentation containing the results here.

[kdahlquist]

• generate new charts dealing with the threshold b issue #289
• fix assorted labeling issues.

[bklein7]

The bar chart analysis PowerPoint Presentation was updated to reflect the changes requested above. Specifically, threshold_b values for genes with no inputs (ABF1, GCR2, ZAP1) were adjusted to zero, and the language used in the chart legends was corrected.

I attempted to add the results from @Nwilli31's CIN5 model runs but could not find these output sheets posted in the Dahlquist Lab repository. Are they uploaded? And if so, should I include the data from both the 14 and 17 gene CIN5 networks?

[kdahlquist]

@Nwilli31 will need to respond about the location of the output sheets. When they are posted, please do the analysis for both networks.

[Nwilli31]

I've uploaded the documents to the Dahlquist Repository. I can do the analysis for the two networks. I created an Excel file with all the strains' optimized production rates and threshold b values because I did not see on compiled in the Dahlquist Repository. The newest powerpoint can be found in the repository.

[bklein7]

I looked at @Nwilli31's updates to the bar chart analysis powerpoint and noticed some issues. Primarily, the corrections made to account for the erroneous threshold_b values (#289) were not carried forward in the new powerpoint. I presume this is because @Nwilli31 did not see my excel file with the bar chart data and made a new one (for reference, this file is in the 15-gene_networks_analysis folder in the Dahlquist Lab repository). I have corrected for this issue and made a few other changes to the powerpoint, which is available here.

[kdahlquist]

This is done, so closing.