GRNmap Testing Report .xlsx vs. .xls 2015-05-27: Difference between revisions

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*Code Version: "current" version from Dr. Fitzpatrick 2014-09-18
*Code Version: "current" version from Dr. Fitzpatrick 2014-09-18
*[https://github.com/kdahlquist/GRNmap/archive/v1.0.6.zip GRNmap] version 1.0.6
*[https://github.com/kdahlquist/GRNmap/archive/v1.0.6.zip GRNmap] version 1.0.6
*[[Media:NW Input 21 Gene Network Sigmoid Model Estimate All Strains.xlsx| Example Input Sheet for Estimation]]
*MATLAB Version: 2014b
*MATLAB Version: 2014b
*Model was run on the following computer: Row#2 4  
*Model was run on the following computer: Row#2 4  


==Input, Output, and Plots==
==Input, Output, and Plots==
*[[Media:22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph]]
*[[Media:22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph]]
==Methods==
==Methods==
=== Preparing the input sheets ===
# Download [[Media:22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph]] and [[Media:22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph]] from a previous experiment [[GRNmap Test Inputs| comparing the sixteen possible options for the input sheet]].
# Both of these files should be in .xlsx format. Open them in Microsoft Excel, enable editting and save as an .xls file.
# Upload the input sheets to openwetware.
===Running GRNmap===
# 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. 
#* Save it into a new folder called "GRNmap" on the Desktop.
#* Unzip the file by right-clicking on it and choosing 7-zip > Extract here.
# 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.
# Click on the green triangle "Run" button to run the model.
#* 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.
#* 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.
#* 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 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 output sheet and the zipped folder with the output plots onto openwetware.
# After the initial run, type the commands "clear all" and "close all" then "GRNmodel" and select the input sheet to run.
==Observations==
==Observations==


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

Revision as of 10:29, 28 May 2015

GRNmap Testing Report

  • Date started: 2015-05-27
  • Code Version: "current" version from Dr. Fitzpatrick 2014-09-18
  • GRNmap version 1.0.6
  • MATLAB Version: 2014b
  • Model was run on the following computer: Row#2 4

Input, Output, and Plots

Methods

Preparing the input sheets

  1. Download 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph and 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph from a previous experiment comparing the sixteen possible options for the input sheet.
  2. Both of these files should be in .xlsx format. Open them in Microsoft Excel, enable editting and save as an .xls file.
  3. Upload the input sheets to openwetware.

Running GRNmap

  1. Download the current version of GRNmap from GitHub, in this case we are using version 1.0.6.
    • Save it into a new folder called "GRNmap" on the Desktop.
    • Unzip the file by right-clicking on it and choosing 7-zip > Extract here.
  2. 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.
  3. Click on the green triangle "Run" button to run the model.
    • 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.
    • Note that the Open dialog will default to show files of *.xlsx only. If your file is saved as *.xls, you will need to select the drop-down menu to show all files.
    • 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.
  4. 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 *.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."
  5. Upload the output sheet and the zipped folder with the output plots onto openwetware.
  6. After the initial run, type the commands "clear all" and "close all" then "GRNmodel" and select the input sheet to run.

Observations

Dahlquist Lab Navigation

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