BIOL388/S25:Week 12

This page is currently under construction.

Input Workbook Trouble-shooting

• If a transcription factor does not have a degradation rate, use the value "If a transcription factor does not appear in the file above, use the value "0.0272" for the degradation rate." for the degradation rate.
• Use 2*"0.0272" for the production rate.

Dynamical Systems Modeling of your Gene Regulatory Network

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 R2024b installed on your computer. It will only work on Windows, not on MacOS.
  1. Download the GRNmap v1.10 code from the GRNmap Downloads page.
     • This is a direct link to start downloading (81 MB).
  2. Unzip the file. (Right-click, 7-zip > Extract here)
  3. Launch MATLAB R2024b.
  4. Open GRNmodel.m, which will be in the directory that you unzipped GRNmap-1.10 > matlab
  5. Click the Run button (green "play" arrow).
  6. You will be prompted to select your input workbook.
  7. You will see an optimization diagnostics graphic that shows the progress of the estimation.
  8. When the run is over, expression plots will display.
  9. 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.
  10. 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.
• You can upload your output .xlsx file into GRNsight beta to visualize the results!