GRNmap Testing Report Identical Runs with Same Code Version and Same Input Workbook 2015-06-01: Difference between revisions

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===GRNmap Testing Report===
===GRNmap Testing Report===
*Date started: 2015-06-01
*Date started: 2015-06-01
*Code Version: "current" version from Dr. Fitzpatrick 2014-09-18
*GRNmap code: GRNmap-beta branch downloaded from Github at 4:20 am 2015-06-01
*[https://github.com/kdahlquist/GRNmap/archive/v1.0.6.zip GRNmap] version 1.0.6
*MATLAB Version: 2014b
*MATLAB Version: 2014b
*Model was run computer (from door): Row#2 4
*Model was run computer (from door): Row#2 4


==Input, Output, and Images==
==Input, Output, and Images==
*[[Media:22-genes 47-edges Dahlquist-data Sigmoidal estimation fixb-0 fixP-0 graph.xlsx| 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph]]
 


==Methods==
==Methods==
# Download the current version of [https://github.com/kdahlquist/GRNmap/archive/v1.0.6.zip GRNmap] from GitHub, in this case we are using version 1.0.6.
# Download the GRNmap-beta branch version from Github by downloading the zip file.  
#* Save it into a new folder called "GRNmap" on the Desktop.
# Move it to the desktop and unzip by right-clicking on it and choosing 7-zip > Extract here.
#* Unzip the file by right-clicking on it and choosing 7-zip > Extract here.
# Open the unzipped "GRNmap-beta branch" folder and find the folder "test_files"
# Drag the two input sheets into the "matlab" subfolder of "GRNmap-1.0.6".  
#*Select two input files to study: "4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph.xlsx" and "4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph"
# Open the "GRNmap-1.0.6" folder and open the "matlab" subfolder.  Double-click on the file "GRNmodel.m" to open GRNmap in MATLAB 2014b.
#Make two copies of each by right clicking selecting copy and then paste.  
# Click on the green triangle "Run" button to run the model.
#*Add _copy-1 or _copy-2 to the end of the name of the copies, then drag to the "matlab" subfolder in "GRNmap-beta"
#* You will be prompted by an Open dialog to find your input file that you created in the previous section.  Browse and select this input file and click OK.
# Open MATLAB and navigate to the "matlab" subfolder in the "GRNmap-beta" folder on the desktop
#* Note that the Open dialog will default to show files of <code>*.xlsx</code> only.  If your file is saved as <code>*.xls</code>, you will need to select the drop-down menu to show all files.
# In MATLAB type the command "GRNmodel" and select the input sheet of study
#* A window called "Figure 1" will appear.  The counter is showing the number of iterations of the least squares optimization algorithm.  The top plot is showing the values of all the parameters being estimated.  You should see some movement of the diamonds each time the counter iterates.
# Once the model has finished running, plots showing the expression over time for all of the genes in the network will appear if "makeGraphs" was set to 1. The plots will automatically be saved as <code>*.jpg</code> files in the same folder as your input file.  Compile the figures into a folder following the naming convention described earlier. Compress this folder by right clicking then selecting "7-zip" and "Add to archive...". Make sure the archive format is "zip."
# Once the model has completed its run, plots showing the expression over time for all of the genes in the network will appear if "makeGraphs" was set to 1. The plots will automatically be saved as <code>*.jpg</code> files in the same folder as your input file.  Compile the figures into a folder following the naming convention described earlier. Compress this folder by right clicking then selecting "7-zip" and "Add to archive...". Make sure the archive format is "zip."
# Upload the .xlsx output sheet and the zipped folder with the output plots onto openwetware.
# Upload the output sheet and the zipped folder with the output plots onto openwetware.
# In between each run type "close all" and "clear all" into MATLAB
# After the initial run, type the commands "clear all" and "close all" then "GRNmodel" and select the input sheet to run.


==Data & Observations==
==Data & Observations==


{{Template:Tessa A. Morris ELN}}
{{Template:Tessa A. Morris ELN}}

Revision as of 16:29, 1 June 2015

GRNmap Testing Report

  • Date started: 2015-06-01
  • GRNmap code: GRNmap-beta branch downloaded from Github at 4:20 am 2015-06-01
  • MATLAB Version: 2014b
  • Model was run computer (from door): Row#2 4

Input, Output, and Images

Methods

  1. Download the GRNmap-beta branch version from Github by downloading the zip file.
  2. Move it to the desktop and unzip by right-clicking on it and choosing 7-zip > Extract here.
  3. Open the unzipped "GRNmap-beta branch" folder and find the folder "test_files"
    • Select two input files to study: "4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph.xlsx" and "4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph"
  4. Make two copies of each by right clicking selecting copy and then paste.
    • Add _copy-1 or _copy-2 to the end of the name of the copies, then drag to the "matlab" subfolder in "GRNmap-beta"
  5. Open MATLAB and navigate to the "matlab" subfolder in the "GRNmap-beta" folder on the desktop
  6. In MATLAB type the command "GRNmodel" and select the input sheet of study
  7. Once the model has finished running, plots showing the expression over time for all of the genes in the network will appear if "makeGraphs" was set to 1. The plots will automatically be saved as *.jpg files in the same folder as your input file. Compile the figures into a folder following the naming convention described earlier. Compress this folder by right clicking then selecting "7-zip" and "Add to archive...". Make sure the archive format is "zip."
  8. Upload the .xlsx output sheet and the zipped folder with the output plots onto openwetware.
  9. In between each run type "close all" and "clear all" into MATLAB

Data & Observations

Dahlquist Lab Navigation

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