Jcowan4 Journal Week 10 - Revision history

Jcowan4: /* Data and Files */ updated file

2019-11-07T01:17:54Z

‎Data and Files: updated file

2019-11-07T01:16:39Z

‎Methods: deleted results and put it together with methods

2019-11-07T01:16:12Z

‎Results

2019-11-07T01:15:57Z

‎Methods: pasted part 9 - final

2019-11-07T01:13:14Z

‎Methods: part 8

2019-11-07T01:12:51Z

‎Methods: part 7

2019-11-07T01:12:29Z

‎Methods: part 6

2019-11-07T01:12:06Z

‎Methods: pasted part 5

2019-11-07T01:11:42Z

‎Methods: pasted part 4

2019-11-07T01:11:15Z

‎Methods: pasted part 3

← Older revision		Revision as of 01:17, 7 November 2019
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	[[Media:GRNMap_WT_Cowan.xlsx \| GRN Map]]		[[Media:GRNMap_WT_Cowan.xlsx \| GRN Map]]
		+
		+	[[Media:GRNMap_WT_Cowan.xlsx \| GRN Map (Updated)]]

	==Conclusion==		==Conclusion==

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 The purpose was to build experience with database queries and making models. This was done to prepare us for our final assignment.
-==Methods==
+==Methods/Results==
 ==== Creating the GRNmap Input Workbook ====

← Older revision		Revision as of 01:16, 7 November 2019
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	'''''Stopping point for the Week 10 assignment.'''''		'''''Stopping point for the Week 10 assignment.'''''

−	~~==Results==~~
	==Data and Files==		==Data and Files==

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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.
 ==Results==

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 ** Strain: A row containing a list of all of the strains for which there is expression data in the workbook.  Should correspond to the "STRAIN" portion of the names of the STRAIN_log2_expression sheets for each strain.  Note that GRNmap will run the model for the wild type network (all genes present in the network) and for networks where the gene deleted from the designated STRAIN has been deleted from the network.
 ** simulation_timepoints: A row containing a list of the time points at which to evaluate the differential equations to generate the simulated data.  This does not need to correspond to the actual measurement times, but should be in the same units (e.g. minutes).
 ==Results==

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 * These are the initial guesses for the estimation of the weight parameters, ''w''.
 * Since these weights are initial guesses which will be optimized by GRNmap, the content of this sheet can be identical to the "network" sheet.
 ==Results==

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 ** The transcription factor names should correspond to the "id" in the other sheets in the workbook.  They should be capitalized the same way and occur in the same order along the top and side of the matrix.  The matrix needs to be symmetric, i.e., the same transcription factors should appear along the top and left side of the matrix.  The genes should be listed in the same order in all the sheets in the Excel workbook.
 ** Each cell in the matrix should then contain a zero (0) if there is no regulatory relationship between those two transcription factors, or a one (1) if there is a regulatory relationship between them. Again, the columns correspond to the transcription factors and the rows correspond to the target genes controlled by those transcription factors.
 ==Results==

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 * It is tedious to copy and paste all of these data by hand, so we will execute a query in Microsoft Access to do it for you.  Follow the steps listed for the "production_rates" sheet for each strains expression data.  After you import the data into Excel, you will need to change the column headers to "15", "15", etc., as described above.
 * Missing values in the expression data sheets are OK; you don't need to put any values there like you did for the production_rates or degradation_rates sheets.
 ==Results==

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 * Again note, the genes should be listed in the same order in all the sheets in the Excel workbook.
 * If there are missing values, substitute the value <code>0.0990</code> for the missing degradation rates.
 ==Results==

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 * If there are missing values, substitute the value <code>0.1980</code> for the missing production rates.
 * Note that the genes should be listed in the same order in all the sheets in the Excel workbook.
 ==Results==