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
*GRNmap code: GRNmap-beta branch downloaded from Github at 4:20 am 2015-06-01
*GRNmap code: GRNmap-beta branch downloaded from Github at 4:20 pm 2015-06-01 (most current version has changed (strain) sheet to (strain)_log2_expression, which has not been done
*MATLAB Version: 2014b
*MATLAB Version: 2014b
*Model was run computer (from door): Row#2 4
*Model was run computer (from door): Row#2 4

Revision as of 16:48, 1 June 2015

GRNmap Testing Report

  • Date started: 2015-06-01
  • GRNmap code: GRNmap-beta branch downloaded from Github at 4:20 pm 2015-06-01 (most current version has changed (strain) sheet to (strain)_log2_expression, which has not been done
  • 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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