Milestone walkthrough (Sept 30, 2019) - GaloisInc/AMIDOL GitHub Wiki

A demonstration video walking through this example has been included with this delivery. Refer to this video if any step is confusing.

Extracting a model from a Julia code file

  • Load the AMIDOL UI in a web browser (we recommend Google Chrome, it is not well tested in other browsers).
  • Click the “LOAD JULIA CODE” button in the top-right of the browser window.
  • Choose a julia code file to upload. Our demo includes a file called SIRS.julia which is the basis for this demonstration. After the code is loaded (which will take a couple seconds), graph icons and arrows representing the Julia code will appear in the main section of the browser window.
  • Drag nodes to position them as desired.
  • Double click a node in the graph to rename it.
  • Double click a palette icon at the top of the window (not in the graph) to change its properties. E.g.:
    • Double click the Orange “question mark” icon to edit it.
    • Use the dropdown menu labeled “Icon:” to assign a new icon like “Cure”.
    • Click the color swatch (likely colored black by default) next to this “Icon:” dropdown to choose a new color.
    • When finished, click the “UPDATE EXISTING ELEMENT” button at the bottom of the popup.
    • You should see the palette and graph have been updated to reflect your new choices.
  • Click the “EXECUTE” button in the top-right to compile the model into an executable and visualize the results.

Comparing Model Results to Experimental Data

  • Load the AMIDOL UI in a web browser (we recommend Google Chrome, it is not well tested in other browsers).
  • Click the “Reset” button in the top-right of the browser window (between the undo and redo buttons to clear out previous simulation results.
  • Next, we’ll load up a pre-baked model of an SIR model with two parallel infection states
    • Download the SIIR.json file.
    • Click on the “Load model file” button and select the file you just downloaded.
  • Click the “EXECUTE” button in the top-right to compile the model into an executable and visualize the results.
  • Now, open up the model comparison page. Here, we are going to compare the total infected population to some (synthetic) reference data
  • Click on “Add to comparison” and enter “Sum infected (model)”
    • Click on the three dots in the “Data traces” column to add a data trace whose name looks like “Infected_scipy”. This is the first infected population.
    • Click on the three dots again to add a data trace whose name looks like “Infected2_scipy”. This is the second infected population.
  • Now, we will load up some data meant to represent statistics on the total infected population.
    • Download the SIIR_infection_rates_demo.json data file
    • In the “Upload new data trace” section, enter “reference dataset”, browse and select the file you just downloaded, and click “Upload trace”
  • Click on “Add to comparison” but this time call the trace “Total infected (reference)”
    • Click on the three dots in the “Data traces” column and select the data trace case “reference dataset” (aka. the data you just uploaded)
  • Finally, click on “Plot the comparison” to bring up a graph that compares the total infected population that your model predicted with the one that was measured.
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