Msamdars Week 10 - Revision history

Msamdars: /* References */ format

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‎References: format

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‎Methods/Results: formatting

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‎Acknowledgments: add sig

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‎Conclusion: add image and conclusion

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‎Data & Files: edit

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‎Data & Files: add output file

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‎optimization_parameters sheet: modify to fit my needs

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‎Data and Files: remove section

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‎Methods/Results: add methods

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 ==References==
 # LMU BioDB 2019. (2019). Week 10. Retrieved October 29, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10
-=# MediaWiki (2019). Category: Help. Retrieved October 29, 2019, from https://www.mediawiki.org/wiki/Category:Help
+# MediaWiki (2019). Category: Help. Retrieved October 29, 2019, from https://www.mediawiki.org/wiki/Category:Help

← Older revision		Revision as of 01:06, 7 November 2019
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	==Methods/Results==		==Methods/Results==
−	==== Creating the GRNmap Input Workbook ====	+	===Creating the GRNmap Input Workbook===

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 Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
-[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 19:03, 30 October 2019 (PDT)
+[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 17:06, 6 November 2019 (PST)
 ==Other Links==

← Older revision		Revision as of 01:05, 7 November 2019
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	==Conclusion==		==Conclusion==
		+	[[Image:BIOL367 F19 dCIN5 GRNMAP MS output.png\|300px\|thumb\|GRNsight visualization of the GRNmap simulation]]

		+	The analysis that we did with our previous data gave us an unweighted network. This showed us the basic linkages within the network. This week, we continued our analysis and carried out an estimation of the network using various mathematical parameters to help estimate the levels of activation and repression. After inputting estimated gene production, mRNA half-life data, and the log2 expression data, GRNmap is a differential equation solver that will give us its estimated level of overall activation and repression. This can be seen on the right. We can see that GCN4 plays a heavy role in down-regulating LYS14, CIN5 heavily up-regulates HAP4, and MET32 down-regulates MET28 substantially. Furthermore, the node-coloring shows that RPN4 was heavily down-regulated, but the lack of a significant connection to another node in the network means that we may look elsewhere for the source of that down-regulation.

	==Acknowledgments==		==Acknowledgments==

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 ==Data & Files==
 [[Media:BIOL367 F19 dCIN5 MS GRNMAPInput.xlsx|dCin5_MS GRNmap Input Spreadsheet]]
-[[Media:BIOL367 F19 dCIN5 MS GRNmapOutput.zipdCin5_MS GRNmap Output Files]]
 ==Conclusion==

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 * The optimization_parameters sheet should have two columns (from left to right) entitled, "optimization_parameter" and "value".
-* You should copy this worksheet from the [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/15-genes_28-edges_sample_Sigmoid_estimation_2019.xlsx sample workbook] provided.  The only row that you need to modify is row 15, "Strain".  Include just the strain designations for which you have a corresponding STRAIN_log2_expression sheet.  If you don't have the dgln3, dhap4, or dcin5 expression sheets, then you will delete those from this row.  If you do so, make sure that you don't leave any gaps between cells.
+* You should copy this worksheet from the [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/15-genes_28-edges_sample_Sigmoid_estimation_2019.xlsx sample workbook] provided.  The only row that you need to modify is row 15, "Strain". Include the dgln3, dhap4, and dcin5 expression sheets. Don't leave any gaps between cells.
 * What follows below is an explanation of what the optimization_parameters mean.
 ** alpha: Penalty term weighting (from the L-curve analysis)

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 ** The left-most column should contain the header "id" and list the standard names for the genes in the model in the same order as in the other sheets.
 ** The second column should have the header "threshold_b" and should contain the initial guesses, we are going to use all 0.
 === Dynamical Systems Modeling of your Gene Regulatory Network ===

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 ==Purpose==
+This week we will continue our experience working with GRNmap. This will continue our learning how to query databases and how to work with a biological data processing pipeline.
 ==Methods/Results==