Cdomin12 Week 10 - Revision history

Cdomin12: /* Purpose */ added

2019-11-07T05:26:48Z

‎Purpose: added

Cdomin12: /* Conclusion */ added

2019-11-07T05:25:52Z

‎Conclusion: added

Cdomin12: /* Data and Files */ added grn map output files

2019-11-07T03:48:05Z

‎Data and Files: added grn map output files

Cdomin12: /* References */ added sig

2019-11-07T03:37:51Z

‎References: added sig

Cdomin12: /* Data and Files */ added description

2019-11-07T03:37:28Z

‎Data and Files: added description

Cdomin12: /* Conclusion */ added acknowledgements and ref

2019-11-05T23:56:12Z

‎Conclusion: added acknowledgements and ref

Cdomin12: /* Purpose */ added

2019-11-05T23:54:51Z

‎Purpose: added

Cdomin12: /* optimization_parameters sheet */ past tense

2019-11-05T23:52:43Z

‎optimization_parameters sheet: past tense

Cdomin12: /* Dynamical Systems Modeling of your Gene Regulatory Network */ past tense

2019-11-05T23:51:45Z

‎Dynamical Systems Modeling of your Gene Regulatory Network: past tense

Cdomin12: /* Data and Files */ delted

2019-11-05T23:50:01Z

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@@ Line 2: / Line 2: @@
 ==Purpose==
-To create a sample workbook in order for it to be correctly uploaded to MATLAB for analysis of gene data.
+To create a workbook of collected data sheets in order for it to be correctly uploaded to MATLAB for modeling of gene data and GRNmap.
 ==Methods & Results==

@@ Line 139: / Line 139: @@
 ==Conclusion==
+A workbook was successfully created so that a Dynamical Systems Modeling of my Gene Regulatory Network could be created. GRNmap worked successfully with the software to yield the modeling data. This will be used to further analyze how cold shock and cold shock recovery work specifically with the genes and transcription factors that were chosen.
 ==Acknowledgments==

← Older revision		Revision as of 03:48, 7 November 2019
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	[[Media:CDGRNmapInput.xlsx \| GRNmap Input Workbook]]		[[Media:CDGRNmapInput.xlsx \| GRNmap Input Workbook]]
		+
		+	[[Media:CD Week 10.zip \| GRNmap Output Files]]

	==Conclusion==		==Conclusion==

← Older revision		Revision as of 03:37, 7 November 2019
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	==References==		==References==
	*Week 10. Retrieved November 6, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10		*Week 10. Retrieved November 6, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10
		+
		+	[[User:Cdomin12\|Cdomin12]] ([[User talk:Cdomin12\|talk]]) 19:37, 6 November 2019 (PST)

@@ Line 132: / Line 132: @@
 ==Data and Files==
 [[Media:CDRegulationMatrix Documented11-4.xlsx |Week 9 Matrix GRNsight Edited]]
-[[Media:CDGRNmapInput.xlsx |GRNmap Input Workbook]]
+[[Media:CDGRNmapInput.xlsx | GRNmap Input Workbook]]
 ==Conclusion==

← Older revision		Revision as of 23:56, 5 November 2019
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	==Conclusion==		==Conclusion==
		+
		+
		+	==Acknowledgments==
		+	1. I worked with [[User:Knguye66]], [[User:Jcowan4]], and [[User:Mavila9]] for this assignment.
		+
		+	2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
		+	[[User:Cdomin12\|Cdomin12]] ([[User talk:Cdomin12\|talk]]) 15:56, 5 November 2019 (PST)
		+
		+	==References==
		+	*Week 10. Retrieved November 6, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10

← Older revision		Revision as of 23:54, 5 November 2019
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	==Purpose==		==Purpose==
		+	To create a sample workbook in order for it to be correctly uploaded to MATLAB for analysis of gene data.

	==Methods & Results==		==Methods & Results==

@@ Line 85: / Line 85: @@
 ==== optimization_parameters sheet ====
-* The optimization_parameters sheet should have two columns (from left to right) entitled, "optimization_parameter" and "value".
+* The optimization_parameters sheet had  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.
+* Copied 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. Included just the strain designations for which you have a corresponding STRAIN_log2_expression sheet. Deleted dzap.
 * What follows below is an explanation of what the optimization_parameters mean.
 ** alpha: Penalty term weighting (from the L-curve analysis)

@@ Line 113: / Line 113: @@
 === Dynamical Systems Modeling of your Gene Regulatory Network ===
-Now you are ready to run the model and analyze the results.  The software we will use is called GRNmap, which stands for Gene Regulatory Network Modeling and Parameter Estimation.  It is written in MATLAB and can be run from code or run as a stand-alone executable if you don't have MATLAB installed.  However, it can only be run in Windows, not on Macs.
+* To run GRNmap from code,installed on computer.
-* To run GRNmap from code, you must have MATLAB R2014b installed on your computer.
+*# Downloaded the GRNmap v1.10 code from the [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap Downloads page].
 *#* [https://github.com/kdahlquist/GRNmap/archive/v1.10.zip This is a direct link to start downloading (81 MB).]
-*# Unzip the file. (Right-click, 7-zip > Extract here)
+*# Unziped the file. (Right-click, 7-zip > Extract here)
-*# Launch MATLAB R2014b.
+*# Launched MATLAB R2014b.
-*# Open GRNmodel.m, which will be in the directory that you unzipped GRNmap-1.10 > matlab
+*# Opened GRNmodel.m, which will be in the directory that you unzipped GRNmap-1.10 > matlab
-*# Click the Run button (green "play" arrow).
+*# Clicked the Run button (green "play" arrow).
-*# You will be prompted to select your input workbook.
+*# Prompted to select your input workbook.
 <!--* To run the GRNmap executable, you must have administrator rights on your computer for installing software.
-** Download the GRNmap v1.10 executable from the [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap Downloads page].
+** Downloaded the GRNmap v1.10 executable from the [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap Downloads page].
 ** [https://github.com/kdahlquist/GRNmap/releases/download/v1.10/GRNmap-v1.10.zip This is a direct link to start downloading (688 MB)]-->
-*# You will see an optimization diagnostics graphic that shows the progress of the estimation.
+*# Saw an optimization diagnostics graphic that showed the progress of the estimation.
-*# When the run is over, expression plots will display.
+*# When the run was over, expression plots displayed.
-*# Output .xlsx and .mat files will be saved in the same folder as your input folder, along with .jpg files containing the optimization diagnostic and individual expression plots.  Save these files.
+*# Output .xlsx and .mat files were saved in the same folder as your input folder, along with .jpg files containing the optimization diagnostic and individual expression plots.  Saved these files.
-*# Note that if you need to run GRNmap again, you should not use the same directory for the input file.  Currently, GRNmap will overwrite previous output.
+* Uploaded output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results!
 ==Data and Files==

@@ Line 110: / Line 110: @@
 ** The left-most column contained 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 had the header "threshold_b" and  contained the initial guesses, we used 0.
 === Dynamical Systems Modeling of your Gene Regulatory Network ===