Eyoung20 journal week 10 - Revision history

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‎Dynamical Systems Modeling of your Gene Regulatory Network: adding tenses and steps

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 ==Acknowledgements==
-I would like to acknowledge my home work partners  [[user:Imacarae|Ivy]], [[user:Dmadere|Delisa]], and [[user:Msamdars|Mihir]] with there help with checking our work and helping to answer questions about the procedure. Also [[user:Ntesfaio|Naomi for her help by answering some questions I had while we were both in lab. I would like to acknowledge that the methods were taken from week 10 and then adapted to fit the actual lab methods preformed. I would like to acknowledge Dr. Dahlquist for her instruction on the topic and the procedure.
+I would like to acknowledge my home work partners  [[user:Imacarae|Ivy]], [[user:Dmadere|Delisa]], and [[user:Msamdars|Mihir]] with there help with checking our work and helping to answer questions about the procedure. Also [[user:Ntesfaio|Naomi for her help by answering some questions I had while we were both in lab. I would like to acknowledge that the methods were taken from week 10 and then adapted to fit the actual lab methods preformed. I would like to acknowledge Dr. Dahlquist for her instruction on the topic and the procedure. Also for her help in troubleshooting the workbook when it did not run in MATlab.
 "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 ==References==
 LMU BioDB 2019. (2019). Week 10. Retrieved November 4, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10
 {{Template:eyoung20}}

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 ==Purpose==
-The goal of this weeks exercise is to prepare the data that has been collected since week 7 in the proper formatting within an excel worksheet. This worksheet will then be run through the grnsight program.
+The goal of this weeks exercise is to prepare the data that has been collected since week 7 in the proper formatting within an excel worksheet. This worksheet will then be run through the grnsight program. Then to collect the visual results of the gene regulatory network after it is run through the program.
 ==Methods==

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 === Dynamical Systems Modeling of your Gene Regulatory Network ===
 * To run GRNmap from code, had to have MATLAB R2014b installed on computer.
 *# Downloaded the GRNmap v1.10 code from the [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap Downloads page].
@@ Line 133: / Line 131: @@
 *# Saw an optimization diagnostics graphic that shows the progress of the estimation.
 *# There were errors that occured in attempting to run this on Tuesday 11/5. [[user:Kdahlquist|Dr. Dahlquist]] is going to trouble shoot to figure out the issue with the input.
-*# When the run is over, expression plots will display.
+*##[[user:Kdahlquist|Dr. Dahlquist]] was able to find and correct the error in the workbook file.
-*# 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.
+*# When the run was over, expression plots were displayed.
-*# 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.
+*# Output .xlsx and .mat files were be saved in the same folder as the input folder, along with .jpg files containing the optimization diagnostic and individual expression plots. These files were saved.
 ==Data and Files==

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 ==Conclusion==
-So far in this weeks lab work all the data for the dCIN5 profile #2 gene regulatoryy network has been complied. Then it was formated to be compatable to the grnsight program. The data will be run through the program to create a model of the gene regulatory network.
+So far in this weeks lab work all the data for the dCIN5 profile #2 gene regulatoryy network has been complied. Then it was formated to be compatable to the grnsight program. The data will be run through the program to create a model of the gene regulatory network. The program was successfully run through the GRNsight modeling software using MATlab. This resulted in a visual representation of the gene network.
 ==Acknowledgements==

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 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.
+* To run GRNmap from code, had to have MATLAB R2014b installed on computer.
-*# Download the GRNmap v1.10 code from the [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap Downloads page].
+*# 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)
+*# Unzipped 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
+*# Open GRNmodel.m, which was in the directory that was 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.
+*# then there was a prompt 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.
+*# Saw 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.

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 ** The left-most column contained the header "id" and listed the standard names taken from the earlier sheets in the workbook so that they were in the same order as in the other sheets.
 ** The second column had the header "threshold_b" and contained the initial guesses, used all 0 for this column.
 ==Data and Files==