"QuizID"	"AppID"	"AppTitle"	"TaskID"	"TaskText"	"RecordID"	"Record"	"Type"	"Note"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	1	"Run the simulation with the pre-set parameter values. It runs the deterministic model and you should see an infection happening. Switch to the stochastic model (under _Models to run_) with the same parameter settings and run the stochastic model. You should see no infection. Change the random number seed to 122 and re-run. You should get an infection. 


Now, set _Models to run_ to both. You should get infections from each model; however, they look somewhat different. The infection produced by the stochastic model takes off faster. It also leads to slightly more infected cells. Figure out how you can determine the total number of infected cells caused by the infection. Hint: The maximum number of infected cells is not the same as the total number. Another hint: Contemplate what happens to the uninfected cells, and therefore what the final value of the uninfected cells might tell you about the infected cells."	"T1R1"	"Total number of infected cells for ODE model"	"Rounded_Integer"	"Report the rounded integer"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	1	"Run the simulation with the pre-set parameter values. It runs the deterministic model and you should see an infection happening. Switch to the stochastic model (under _Models to run_) with the same parameter settings and run the stochastic model. You should see no infection. Change the random number seed to 122 and re-run. You should get an infection. 


Now, set _Models to run_ to both. You should get infections from each model; however, they look somewhat different. The infection produced by the stochastic model takes off faster. It also leads to slightly more infected cells. Figure out how you can determine the total number of infected cells caused by the infection. Hint: The maximum number of infected cells is not the same as the total number. Another hint: Contemplate what happens to the uninfected cells, and therefore what the final value of the uninfected cells might tell you about the infected cells."	"T1R2"	"Total number of infected cells for stochastic model (_rngseed_ = 122)"	"Integer"	"Report the integer"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	2	"With the settings as they just were, increase the number of simulations (for the stochastic model) to 2, re-run the simulation. Notice that you see two distinct outcomes for the two stochastic simulations. Also, look at the message below the plot (what the app calls an outbreak is what I call an infection here, basically a within-host outbreak). Based on that, make sense of the fact that the average total number of infected cells for the deterministic simulation is much higher than for the stochastic (which contrasts to the finding from the previous task)."	"T2R1"	"Average total number of infected cells for stochastic model"	"Integer"	"Report the integer"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	3	"Set number of simulations to 4, keep everything else the same. You'll get 2 outbreaks. The maximum value for the virus for the stochastic simulations is around half that of the deterministic model. Based on the text below the plot, you know that the stochastic results are the averages over all runs. Thus, you are adding two values that are similar to the ODE model to 2 values that are 0. Reporting the average (mean) over situations that both do and don't lead to infection might not be too insightful. It might be better to report the number/fraction of times you get an infection, and then just the average for some quantities for those simulations where an infection occurs. For these settings, is it true that the average of the virus peak for the stochastic simulations is above that of the ODE? You might want to switch to plotly and zoom in on the peaks to determine this."	"T3R1"	"TRUE or FALSE: The average virus peak for the stochastic simulations that lead to an infection is above the ODE value."	"Logical"	"Report TRUE or FALSE"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	4	"Set _Model to run_ to stochastic, number of simulations 20. Run the simulation. The message under the plot should inform you that for  runs, an infection/outbreak occured. The reason we sometimes do not get an infection is that we start with a single virion, which sometimes, just by chance, goes extinct before the infection can take off. This does never happen for the deterministic model. If the infection starts with more virions, the chance of all of them going extinct is much less. Test that by starting with 5 initial virions, re-run the simulation. You should find 13 outbreaks/infections happening. Repeat for 10 virions. You can explore different random seeds and more simulations to convince yourself that an increase in initial virus leading to more infections is a robust result (and doesn't depend on specific choices of the random seed or number of samples)."	"T4R1"	"Number of outbreaks/infections when starting with 10 virions"	"Integer"	"Report the integer"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	5	"The starting number of virions has a strong impact on the chance an infection occurs. Some model parameters do as well. If the virus is fitter (e.g. higher virus production rate, faster rate of infection), the chances that an infection occurs also increases. Let's try that. 


Reset all inputs. Turn on stochastic simulations. Set to 20 simulations. Run the model. You should now get 4 outbreaks/infections (the random number seed is different from above). Now set p=10. Re-run. The number of infections should have increased. 


Return to p=5 and set b=0.0002. You will again get more outbreaks/infections. Again, play with the random number seed and the number of simulations to convince yourself that this is a general finding."	"T5R1"	"Number of outbreaks/infections for b=0.0002."	"Integer"	"Report the integer"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	6	"With the model settings we explored so far, stochasticity/randomness matters in deciding if an infection occurs or not. Once it has started, the resulting time-series look fairly smooth and not too noisy. The reason for that is that the numbers of virus grows quickly, and there are a lot of cells; thus, in general, the law of large numbers applies and the overall behavior of the system is fairly well approximated by a deterministic model. We can change this by reducing the number of cells. Reset all inputs. Then set U=1000. To make up for this change, increase b to b=0.002. Run 20 simulations of the stochastic model. You will see that the time-series look much noisier, even at the peak. You should find that 4 simulations produce an infection. Record the average number of peak/maximum infected cells.

The important take-home message from this is that for small numbers (e.g., at the start or end of an infection, or when overall numbers are large), stochasticity is often important. Once numbers are fairly large (100s or more), then deterministic models are usually doing a good job describing the system dynamics."	"T6R1"	"Average number peak/max infected cells (round to integer)."	"Rounded_Integer"	"Round to integer"
"DSAIRM_basicvirusstochastic"	"basicvirusstochastic"	"Stochastic Dynamics"	7	"Keep exploring. You can for instance turn on births and deaths of uninfected cells to explore chronic/steady state conditions and see how stochasticity impacts those."	"T7R1"	"Nothing"	"None"	""
