GRNmap Testing Report Executable 2015-06-08 TM

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Test Conditions

  • Date started: 2015-06-03
  • Test Performed by: Tessa A. Morris, Electronic Notebook
  • Code Version: GRNmap v1.0.8
  • MATLAB Version: No Matlab
  • Computer on which the model was run: Biology Department Laptop 1

Purpose

  • The purpose of this test was to make sure that the executable works on a computer without MATLAB.
  • Issue 84

Results

Methods

  1. Open Google Chrome or Firefox and navigate to the GRNmap home page by following this link. Click on the "Downloads" button located in the navigation bar at the left of the screen to go to the Downloads page.
  2. You may have to disable the virus software on your computer because the GRNmap website may not be trusted on all computers. On VirusScan Console, disable the all access protection.
  3. Click "Download GRNmap Executables", find "GRNmap v1.0.8", and then click the green button that says "Download GRNmap_v1.0.8.zip executable" and save the file to the desktop. The computer settings may automatically save the file to the "Downloads" folder. If this is the case, drag the .zip file to the desktop. (theoretically this should work, but did not on either the Kam Dahlquist, GRNmap, or Student accounts with either Chrome or Firefox)
  4. An alternative method of downloading GRNmap is to go to github.com and search "GRNmap" and select "kdahlquist/GRNmap" or follow this link. Select "Releases" and click "GRNmap_v1.0.8.zip". This method should work without changing the security settings of the anti-virus software.
  5. While this is working, create a new folder called "GRNmap_testing_report_executable_2015-06-08".
  6. Download previously created test input sheets from openwetware and save them to the folder you just created. (It may be easier to have these zipped into the executable). There are sixteen different variations of the input sheet created with artificial data to demonstrate the function of the model.
  7. Once "GRNmap_v1.0.8.zip" has been downloaded, extract the zip file by right clicking and selecting the option "Extract All".
  8. The extracted file should be named "GRNmap_v1.0.8". Open this folder, open the subfolder "GRNmap_v1.0.8", and double click the program called "MyAppInstaller_mcr." When prompted select "Run". This may take a few minutes to install.
    • To reinstall GRNmap for testing purposes go to the start menu, select "Control Panel." Search for "Programs and Features." There are two programs that need to be uninstalled "GRNmap" and "MATLAB Compiler Runtime 8.4"
    • Select "GRNmap" and press the button "Uninstall/Change" at the top of the screen. After a moment an uninstaller window will appear that will verify that you want to delete "GRNmap" press "Uninstall." A status bar will show the progress. After uninstalling there is a warning that there may be remaining GRNmap files that can be manually deleted from the programs folder. Press "Finish."
    • Next select MATLAB Compiler Runtime 8.4 and press "Uninstall/Change." A window titled "Uninstall Products" will appear verifying you want to remove MATLAB Compiler Runtime from: C:\Program Files\MATLAB|MATLAB Compiler Runtime\v84. Press "Uninstall." A status bar will show the progress. After the program is uninstalled, there is a warning explaining that there may be some remaining files in C:\Program Files\MATLAB|MATLAB Compiler Runtime\v84 that can be manually deleted. Press "Finish."
    • Go to the start menu, and find "Computer." Navigate to Local Disk (C:) and the subfolder "Program Files." Right click on "GRNmap" and press "Delete." Do the same for the folder "MATLAB"
  9. You will be prompted to an installer window, you must have administrator privileges to install the MATLAB compiler library. When the GRNmap Installer window appears, click "Next" to start the installation process. A dialogue box titled "Preparing Files" will appear with a status bar monitoring the process of the program "Assembling product list...". It will then ask you to designate a installation folder. Accept the default location C:\Program Files\GRNmap. It will warn you that this folder does not exist and ask if you would like to create it. Click "Yes" then press "Next." The next window asks where you would like the "MATLAB Compiler Runtime" installed. Accept the default location C:\Program Files\MATLAB\MATLAB Compiler Runtime. It will warn you that this folder does not exist and ask if you would like to create it. Click "Yes" then press "Next."
  10. Accept the terms of the license agreement by selecting "Yes" and then pressing "Next." On the next screen press "Install" and a status bar will appear. Once the installation is complete, select "Finish".
  11. Navigate to the "GRNmap_v.1.0.8" folder on the desktop and double click the program "GRNmap" and select "Run".
    • For some reason the GRNmap start up screen is in the top right corner of the screen rather than the middle of the screen as it was previously (10:04 am 2015-06-09)
  12. While this is working, create a new folder called "GRNmap_testing_report_executable_2015-06-08".
  13. Download previously created test input sheets from openwetware and save them to the folder you just created. (It may be easier to have these zipped into the executable). There are sixteen different variations of the input sheet created with artificial data to demonstrate the function of the model. The input 4-genes_6-edges_artificial-data Sigmoidal_estimation_fixb-0_fixP-0_graph will best demonstrate all of the features of GRNmap
  14. GRNmap will open a dialogue box called "Select Input Worksheet for Simulation." Navigate to the Desktop and select one of the test input sheets you saved in the "GRNmap_testing_report_executable_2015-06-08" folder.
  15. A Matlab dialogue box called "Figure 1" should pop up on the screen. There should be two plots on the screen following the program's progress, and a counter number.
  16. If you selected an input sheet with the option to make graphs, you will know the model has finished running when the program chimes (if your sound is on) and plots of the four difference genes appear on the screen. If you selected the option "no-graph" you will know the model has finished running when the counter number stops increasing. The counter image ("figure 1"), plots, output .xlsx file, and output .mat file should be save to the folder where the input sheet was saved, "GRNmap_testing_report_executable_2015-06-08". The plots and output sheets can be compared to those run previously. The LSE and penalty term cannot be calculated using the executable.
  17. In order for the program to save the outputs successfully, none of the directories (folder name or administrator name) can have any spaces.
  18. The counter image ("figure 1") must be saved manually, but selecting "File" then "Save As..." and changing the file type to .jpeg, the name to "Counter" and moving it into the "GRNmap_testing_report_executable_2015-06-08" folder. The names of the plots will be named figure then 2, 3, 4, or 5. You must also change the name of these manually, by clicking on the file once and then clicking the name. The current name should be highlighted in blue and you can then type in the name of the gene that was plotted.
    • On computers without MATLAB the .mat file will be classified as a "Microsoft Access Table Shortcut"
  19. Create a subfolder in "GRNmap_testing_report_executable_2015-06-08" with the name of the input file and then add "_plots" (for example 4-genes_6-edges_artificial-data Sigmoidal_estimation_fixb-0_fixP-0_graph_plots) and move the .jpegs to this folder. Zip the folder by right clicking it and selecting "Send to" and then "Compressed (zipped) folder."
  20. To view the file types, go to the start menu, select "Control Panel" and search for "Folder Options" Under the "View" tab uncheck the box next to "Hide extensions for known file types."
  21. We saved and uploaded the input .xlsx, output .xlsx, output .mat (classified as a "Microsoft Access Table Shortcut" ), and zipped folder with the plots to openwetware.

Testing on Student account (without administrator privileges) after being installed on an administrator account

  1. On the start menu, search "GRNmap" and select GRNmap under "Programs"
  2. Download a test file from openwetware and drag into a folder called "GRNmap_executable_2015-06-09"
  3. You will be prompted by MATLAB to select an input file. Navigate to the folder with the test input sheet and select "Open."
  4. A MATLAB figure named "Figure 1" will appear and monitor the progress.
  5. When complete the plots of the individual genes will appear on the screen. They will be saved as .jpegs in the folder that contains your input sheet. They will be named figures 2, 3, 4, and 5.
  6. There will also be a .xlsx output sheet created and a .mat output sheet created. If your computer does not have MATLAB, it will be classified as a Microsoft Access Table Short Cut.

Testing on OS X Yosemite (Version 10.10.1

  1. The zip file could be successfully downloaded and unzipped, but was unable to install the MATLAB compiler library.

Running a larger test file

  1. Reinstall GRNmap by following the procedure above
  2. Download 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx
  3. Drag it to the folder "GRNmap_executable_2015-06-09"
  4. Open GRNmap and select 2-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx
  5. Time how long it takes to run.

Discussion

  • The executable works as long as the computer has administrator privileges and none of the directory names (folder name or administrator name) have any spaces. Anti-virus software also prevented the download of GRNmap from the GRNmap website (http://kdahlquist.github.io/GRNmap/index.html) so it must be disabled for the download to work. However, the anti-virus software did allow downloads from github (https://github.com/kdahlquist/GRNmap).
  • Later on the GRNmap start up screen shifted to the top right hand corner of the screen instead of the middle as it had previously.
  • Each step of the process involving the executable takes a few minutes to work, which may be due to the fact that it was run on an older computer.
  • The executable works even after the laptop has been shut off and the program was not reinstalled.
  • GRNmap will work on a non administrator account if it has been downloaded on an administrator account.
  • The executable is not compatible with OS X Yosemite
  • Executable worked after being uninstalled and reinstalled
  • 29:07.18 for 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx
  • Selected from programs start menu after running once before appeared in top left corner of the screen instead of the center (this happened before, will look into the cause). It also took more time for GRNmap to load and asked for network credentials.
    • Going to the GRNmap_v1.0.8 folder was faster and appeared in the middle of the screen again, but so did selecting it from the start menu.
  • 3:34.52 for 4-genes_6-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx
  • Tried running two at the same time. Ran 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-1_fixP-1_graph.xlsx then 2 minutes later started running 4-genes_6-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx
    • Took 3:43.75 for 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-1_fixP-1_graph.xlsx to run
    • Took ~3:30 for 4-genes_6-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx to run
    • Will run again to verify, but there was a problem with how the plots were saved but the .mat and .xlsx output saved for both
      • Started 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-1_fixP-1_graph.xlsx 24 seconds after starting 4-genes_6-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx
      • Took 3:39 for 4-genes_6-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx (all plots, .mat and .xlsx output)
      • Took 4:32 for 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-1_fixP-1_graph.xlsx (all plots, .mat and .xlsx output)
      • I moved the figures from 4-genes_6-edges_Dahlquist-data_Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx into a folder before 22-genes_47-edges_Dahlquist-data_Sigmoidal_estimation_fixb-1_fixP-1_graph.xlsx output so they didn't overwrite.
    • Running two at a time will produce the output sheets (.mat and .xlsx) as well as the plots, however the figures will overwrite if they are in the same folder.
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