Week 10 - Revision history

Kdahlquist: /* Team Membership */ delete reference to team

2019-11-07T16:41:06Z

‎Team Membership: delete reference to team

Kdahlquist: /* Individual Journal Assignment */ comment out group project category

2019-11-07T16:40:34Z

‎Individual Journal Assignment: comment out group project category

Kdahlquist: /* Overview */ comment out team page

2019-11-07T16:40:10Z

‎Overview: comment out team page

Kdahlquist: /* Dynamical Systems Modeling of your Gene Regulatory Network */ moved stopping point

2019-11-06T00:01:21Z

‎Dynamical Systems Modeling of your Gene Regulatory Network: moved stopping point

Kdahlquist: /* Dynamical Systems Modeling of your Gene Regulatory Network */ add file saving instructions

2019-11-06T00:00:41Z

‎Dynamical Systems Modeling of your Gene Regulatory Network: add file saving instructions

Kdahlquist: /* Dynamical Systems Modeling of your Gene Regulatory Network */ cancel team journal for week 10

2019-11-05T22:28:17Z

‎Dynamical Systems Modeling of your Gene Regulatory Network: cancel team journal for week 10

Kdahlquist: /* Data and Files */

2019-11-05T22:27:32Z

‎Data and Files

Kdahlquist: /* Whole Team Journal Assignment: Creating a Team Wiki Page */ comment out team wiki page

2019-11-05T22:25:41Z

‎Whole Team Journal Assignment: Creating a Team Wiki Page: comment out team wiki page

Kdahlquist: /* network sheet */ fix link

2019-11-01T15:57:17Z

‎network sheet: fix link

Kdahlquist: /* Expression Data Sheets for Individual Yeast Strains */ note that missing values is OK

2019-11-01T15:56:35Z

‎Expression Data Sheets for Individual Yeast Strains: note that missing values is OK

@@ Line 40: / Line 40: @@
-=== Team Membership ===
+=== Homework partners ===
 For creating the GRNmap Input Workbook, the groups will be the same as for the [[Week 9]] assignment.
 ==== Creating the GRNmap Input Workbook ====
 Now that you have identified the gene regulatory network that you want to model, the next step is to generate the input Excel workbook that you will run in the GRNmap modeling software.

@@ Line 29: / Line 29: @@
 ** Link from your user page to this Assignment page.
 ** Link to your journal entry from your user page.
-* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.'''  Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
+<!--* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.'''  Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''-->
 * Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
 * The sections you need for this week's individual journal entry are Purpose, Methods/Results (one combined section), Data & Files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

@@ Line 6: / Line 6: @@
 * To gain experience with database queries and modeling, the last step in preparation for the final project.
 * Everyone will contribute to [[Week_10#Team_Journal_Assignment | Creating your team's home page,]] and in the process, getting yourselves organized for the final project.
 * Coders (and Designer) will then move on to preparing a journal club presentation for Tuesday, November 14 on their assigned papers.
 * QA's and Data Analysts will search the literature and microarray databases for additional papers on the transcriptional response to cold shock in yeast.  (They will prepare their journal club presentations on one of these papers for the [[Week 12]] assignment and deliver the presentation itself on Tuesday, November 21.)

@@ Line 190: / Line 190: @@
 * You can upload your output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results!
-'''''Class/Team Journal Assignment has been cancelled for Week 10. Stopping point for the Week 10 assignment.'''''
+'''''Class/Team Journal Assignment has been cancelled for Week 10.'''''
 ==== Data and Files ====
@@ Line 202: / Line 202: @@
 The files will save automatically after GRNmap is finished running.  You will need to zip them and upload them to the wiki.
 <!--

← Older revision		Revision as of 00:00, 6 November 2019
Line 190:		Line 190:
	* You can upload your output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results!		* You can upload your output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results!

−	Class/Team Journal Assignment has been cancelled for Week 10.	+	'''''Class/Team Journal Assignment has been cancelled for Week 10. Stopping point for the Week 10 assignment.'''''

		+	==== Data and Files ====
		+
		+	Your data and files section should include:
		+	* Your Excel workbook that is your GRNmap input workbook (.xlsx file)
		+	* Your GRNmap output files zipped together should include:
		+	** An .xlsx output file that has the same name as your input file, but with "output" appended to the filename.
		+	** An .mat output file that has the same name as your input file, but with "output" appended to the filename.
		+	** A bunch of .jpg files, one for each gene and one called "optimization_diagnostics.jpg"
		+	The files will save automatically after GRNmap is finished running. You will need to zip them and upload them to the wiki.

← Older revision		Revision as of 22:28, 5 November 2019
Line 189:		Line 189:
	*# 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.		*# 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.
	* You can upload your output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results!		* You can upload your output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results!
		+
		+	Class/Team Journal Assignment has been cancelled for Week 10.
		+

← Older revision		Revision as of 22:27, 5 November 2019
Line 169:		Line 169:

	'''''Stopping point for Tuesday's interim deadline.'''''		'''''Stopping point for Tuesday's interim deadline.'''''
		+
		+	=== 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, you must have MATLAB R2014b installed on your computer.
		+	*# Download 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)
		+	*# Launch MATLAB R2014b.
		+	*# Open GRNmodel.m, which will be in the directory that you unzipped GRNmap-1.10 > matlab
		+	*# Click the Run button (green "play" arrow).
		+	*# You will be 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].
		+	** [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.
		+	*# When the run is over, expression plots will display.
		+	*# 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.
		+	*# 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.
		+	* You can upload your output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results!
		+

	<!--		<!--

@@ Line 278: / Line 278: @@
 * Did LMU pay a fee for this article: no
 -->
 == '''Whole Team Journal Assignment''':  Creating a Team Wiki Page ==
@@ Line 295: / Line 297: @@
 ## What will I do next to fix what didn't work?
 # Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.
+[[Category:Group Projects]]
 [[Category:Assignment]]

@@ Line 120: / Line 120: @@
 ==== network sheet ====
-* The network you derived from the YEASTRACT database for the [[BIOL388/S19:Week 5 | Week 5]] assignment can be copied and pasted into this sheet directly.  You may need to edit the contents of cell A1, but the rest should be good to go (especially since you previewed it in GRNsight). The description below just explains what is already in this worksheet.
+* The network you derived from the YEASTRACT database for the [[Week 9]] assignment can be copied and pasted into this sheet directly.  You may need to edit the contents of cell A1, but the rest should be good to go (especially since you previewed it in GRNsight). The description below just explains what is already in this worksheet.
 ** This sheet contains an adjacency matrix representation of the gene regulatory network.
 ** The columns correspond to the transcription factors and the rows correspond to the target genes controlled by those transcription factors.

@@ Line 116: / Line 116: @@
 * The data you will be using is contained in the [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/Expression-and-Degradation-rate-database_2019.accdb Expression-and-Degradation-rate-database_2019.accdb] file that you used to obtain the production and degradation rates.
 * 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.
 ==== network sheet ====