FAQs for GLEAMviz

These FAQs are not part of the GLEAMviz project. They were constructed from FAQs listed by people who ran the program and are answered by the Pandem Data team. It is intended to be user-friendly. The answers are in simpler terms than would be used by experts in the modeling field.

We hope that you will find these FAQs, the instructions for using the GLEAMviz program, and the information on how to build an infectious disease model helpful.

 

Note: The instruction guides, Using GLEAMviz and Infectious Disease Modeling with GLEAMviz, should be printed in color for better detail, if you and your students are using the instructions in print form. The Visualization Dashboard shows detail more clearly when printed in color. If you cannot download the program, you can still use the activities by printing the pages in color. All details produced by running the infectious disease model are shown on pages included in the activity.

 

How do I solve inconsistencies that appear when I build an infectious disease simulation?
The Inconsistency will tell you what you need to change in order to get your sim to run.  Some examples are:

  • !At least one compartment must be marked as a clinical case.
    • Solution: Click to enable the thermometer icon on a compartment to mark it as a clinical case.
  • !The rate for the spontaneous transition from infectious to recovered to empty. (This inconsistency will show up for the compartments for which you have not yet set rates. Each of these inconsistencies will be solved when values are added.)
    • Solution: Set the rates.  Rates can be constant values or variables that need to be defined in the variables menu.
  • !At least two compartments must be defined.

As you build the model, the inconsistency will appear and then go away when you label or name the compartment.

Why doesn’t my simulation clone when I use the clone option?
The GLEAMviz program seems to experience some “glitches” occasionally as the system updates and as it is being used at that time. If you are doing a demonstration of how the program works, it is a good idea to have a simulation built that you can access from your list of sims.

If you want to build a sim “live” to show a step-by-step approach, knowing how you want to build it and what rates and settings you want to use will reduce the likelihood of getting inconsistencies that you don’t recognize or that don’t solve quickly.

Why doesn’t my simulation run?
If you have any inconsistencies, the sim won’t run. These are displayed on the right side of the Simulation Builder. When all the inconsistencies are fixed, the disease simulation will run.

If you have not set up the model on the Settings page (click the tab at the top of the Sim Builder to set the various descriptions for your simulation), your sim won’t run.

If you get an error message on the “status page”, the server may not be processing sims at that moment. The problem sometimes corrects itself after a few minutes.

If  the GLEAMviz program has been updated and you receive a message when you log in to update, the program may be a little glitchy for the first few runs. It usually works fine after that.

How long will it take me to learn how to use GLEAMviz?
Not that long if you use the step-by-step instruction guides and work through the program a few times. Of course, everyone works at a different pace; it’s hard to give an exact length of time for learning how to use the program.

How do I add a compartment?
Click the ADD COMPARTMENT button at the top left side of the GLEAMviz Simulator interface.

How do I add a name to a compartment?
Click on the “default” name on the compartment and type in the name.

How do I rename a box?
Click on the compartment name and rename.

What do the icons mean on the compartments?

How do I save a copy of my simulation to edit it?
Your simulation is automatically saved. You can access your sims each time you log in to GLEAMviz. You should remember to change the name of the simulation to reflect the outbreak, the date, or even just by numbering so that you can find the simulation you want without going through all the sims you may have built.

What does the yellow triangle with the exclamation point mean?  
It means there is an issue that has to be addressed before your sim will run. You will see this symbol where there is an inconsistency to solve or on the Settings tab if you have not set the descriptors for your disease outbreak.

What compartments do I select to be clinical cases or carriers?

Mark all compartments that may introduce or spread the virus in the population as a clinical case or carrier. For example, it is obvious that the Infected compartment is marked as clinical cases, but what about the Exposed compartment? If people in the Exposed compartment can transition to an infectious state, they could generate transmission to the general population and should be marked as carriers, at least.

When would I choose a spontaneous transition?

Choose a spontaneous transition when you want to model a transition that would move from one compartment to another without the active transmission of an infectious pathogen. For example, the transition of a latent viral infection to an infectious state or the transition of an infectious state to recovered.

When building an infectious disease model and working on the parameters on the settings page, when would I choose a single-run sim vs a multi-run sim? 

A single-run sim displays results from one run of the data and no confidence intervals. But, unlike a multi-run simulations, results include data on concrete transmission of infected individuals between cities which can be shown as arcs in the Visualization Dashboard. Your choice just depends on what you want for that model; it does not affect the resultant spread of infectious disease for your teaching purposes.

How long does it take to run my model?
It depends on how busy the GLEAMviz server is at the time, but it usually only takes a minute or two to run the simulation model. Sometimes, the server is down and you will know that your simulation is not running by looking at the simulation status on the interface.

If the server is very busy, it may take a bit longer to retrieve your results. Your sim is always available on your sim site, so you can always go back and show the dashboard running your infectious disease model.

Expect a slight delay while your sim is running and expect a slight delay when you retrieve your results in order to run the visualization dashboard.

How long will it take me to lean how to use GLEAMviz?

Not that long if you use the step-by-step instruction guides and work through the program a few times. Of course, everyone works at a different pace; it’s hard to give an exact length of time for leaning how to use the program.

How do I know there is problem with the server and that it is not my model that is creating the problem?
You will receive an error message if there is a problem with your sim. You will also see the “!” icon and your problem will be defined.

If there is a server problem, your sim may be listed as “failed” (meaning that sending it to the server failed, not the content of your sim).

Why do compartments appear when I haven’t added them?  What relationships cause the appearance of compartments automatically?
Compartments automatically appear depending on what compartments you build for your simulation and what transmission methods you choose. You will also have to identify the rates of movement through those compartments as well.  Think through what you want the (added) compartment to represent and use the drop-down to choose the type of compartment. Then, set the rate for movement from that compartment to the next.

I’m having trouble setting the numbers on the simulation. How do I know what numbers to use?
This is the tricky part. GLEAMviz uses stochastic (randomly determined) algorithms (set of definite mathematical operations) to mathematically define the numbers of individuals in the groups over times and display the transitions and disease spread visually on a simulation dashboard. The output (your disease “run” shown visually in the Dashboard) depends on what disease parameters you input in the Simulation Builder.

Remember, you are assigning rates of people moving from one compartment to another. For example, assigning a “larger” number to the rate for movement from the Susceptible group to the Infected means there will be a faster disease outbreak. If you want to reflect a disease that that would not have a high infectivity, lower the rate.

It is a good idea to submit different parameters for models and see what results you get from running your own model. As you try different rates, analyze the results of the sim in the Dashboard and see if you need to adjust the rates to reflect the disease example.  Try changing one rate at a time to identify which rate may be incorrect. Rates for different diseases depend on the other criteria you set up; we can’t give you a list of ready-made rates.

It seems like the graphs in the Dashboard change a lot some of the time when only a small change has been made in the rates. Can that be correct?
Yes, but make sure you are analyzing the graphs correctly. The numbers on the axes change depending on the values selected for the sim, including the values you select on the Settings page. If the axes values change, the graph may look greatly different at first glance while there isn’t that much difference in the values being generated.

How do I save a copy of my simulation to edit it?

Your simulation is automatically saved. You can access your sims each time you log in to GLEAMviz. You should remember to change the name of the simulation to reflect the outbreak, the date, or even just by numbering it so that you can find the simulation you want without going through all the sims you have built.

When I run a simulation the analyzer on the Visualization Dashboard does not show transitions for the city in which I seeded the disease. Wouldn’t that city have to have an outbreak? Why doesn’t it show?

Yes, the city would have disease cases. Sometimes the data for the city is so variable/day that you have to turn off other locations you are visualizing in order to see the data for that city. For example, if you are running global data, a U.S. city, and a third city, and the third city doesn’t show, turn off (unclick the boxes) for the global and the U.S. option and the third city’s data should appear.

Where can I get support for using Gleamviz? 

GLEAMviz has a few resources to help you learn how to build disease outbreak simulations.

GLEAMviz Models has examples of models, including SI, SIR, SIS, SEIR and a much more complicated example of the 2009 a (H1N1) Influenza model.
http://www.gleamviz.org/simulator/models/

GLEAMviz Simulator describes some features of the Simulation Builder and Dashboard.
http://www.gleamviz.org/simulator/

How do I get the most information that I can from the model simulation?
Change the settings on the Active Compartments and the New Individuals choices at the bottom right of the Dashboard interface to see and analyze each parameter defined by the Settings page.

For example, just by switching the compartments displayed in the Dashboard, you see what happens to the numbers of individuals affected over time in each group.