Pathogens and pathogen data

[trvrb]

Possible pathogens to look at, roughly sorted in order of preference / data availability:

• HIV (Trevor)
• pneumo (Sarah)
• dengue (Trevor)
• malaria (Sarah)
• enterovirus 71, including Polio (Sarah)
• rotavirus (Sarah)
• norovirus (Trevor)
• coronavirus (Trevor)
• swine flu (Trevor)
• bird flu (Trevor)
• cholera (Sarah)
• Shigella
• Typhoid
• herpes virus, EBV, HSV, etc...

[trvrb]

@sarahCobey ---

Questions:

1. Should we be providing data for some of these pathogens in the repo? I think yes, but is this just links out to papers? Or is it actual data we want people analyzing? We can, of course, encourage google scholar, but I don't think we should rely on this.
2. Are we trying to give groups time at the end of lectures to discuss their pathogen? In which case are there 3 discussion periods, after:
   • Day 1, Session C: Serology and antigenic evolution (Trevor)
   • Day 2, Session A: Timeseries and fitting (Sarah)
   • Day 2, Session C: Selection (Trevor)

for serology, timeseries and trees respectively?

[sarahCobey]

Should we be providing data for some of these pathogens in the repo? I think yes, but is this just links out to papers? Or is it actual data we want people analyzing? We can, of course, encourage google scholar, but I don't think we should rely on this.

Supplying material in the repo will save valuable time in class. Asking people to analyze (i.e., perform computations on) time series and alignments would probably be too much--although maybe there are small exercises we could pick off. I suggest we rely mostly on figures from published papers, or perhaps the papers themselves. I'm still fuzzy on exactly what kinds of inference we expect them to make, but I will try to figure this out in the next day or two.

Are we trying to give groups time at the end of lectures to discuss their pathogen? In which case are there 3 discussion periods, after:

Day 1, Session C: Serology and antigenic evolution (Trevor) Day 2, Session A: Timeseries and fitting (Sarah) Day 2, Session C: Selection (Trevor)

This makes sense. Some groups may not have much to present after some sections, but that's okay. Perhaps they could also speculate what would be necessary for forecasting.

[trvrb]

This makes sense. Some groups may not have much to present after some sections, but that's okay. Perhaps they could also speculate what would be necessary for forecasting.

Ah. So you're thinking for groups to give 3 small reports and then a synthesis on Day 3?

Perhaps they could also speculate what would be necessary for forecasting.

I like it.

---

I think we should plan to give some time on Day 3 morning for groups to synthesize findings and figure out a presentation strategy.

[sarahCobey]

I had assumed (not sure why) that groups would discuss and present after each of those three sessions, but a single synthesis period makes the most sense. If you'd like to move the synthesis period to the end of Day 2 and the forecasting to Day 3, that's fine with me. Both schedules look good.

[trvrb]

I think time wise, we'll need to plan on:

25-30 people / 3-4 people per group = ~8 groups * 10 min per group = 80 min for synthesis presentations.

This would be a full session. I think Day 2 is already quite full. What if we try to do forecasting at the end of Day 2 and synthesis presentations at the beginning of Day 3?

[sarahCobey]

That sounds good. We leave roughly an hour in the forecasting session on Day 2 for them to pull together their presentations.

---

Sarah Cobey, PhD Assistant Professor Ecology & Evolution University of Chicago

(617) 756-7204 (cell) sarahcobey (Skype) cobeylab.uchicago.edu

On Mon, Jul 18, 2016 at 11:48 PM, Trevor Bedford notifications@github.com wrote:

I think time wise, we'll need to plan on:

25-30 people / 3-4 people per group = ~8 groups * 10 min per group = 80 min for synthesis presentations.

This would be a full session. I think Day 2 is already quite full. What if we try to do forecasting at the end of Day 2 and synthesis presentations at the beginning of Day 3?

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[trvrb]

@sarahCobey --- Take a look at this: https://github.com/trvrb/sismid/tree/master/lineup/dengue

Do you think this is right sort of setup? If so, I'll start in on other pathogens tomorrow.

[sarahCobey]

I like it. I can do malaria, rota, pneumo, entero (might not get to it until tomorrow). Perhaps move cholera toward the top. I don't know much about its evolution, but the (bio/sero)types are interesting.

[trvrb]

That's great. Thanks Sarah. I'll work on things that aren't these today.

[trvrb]

Also, I thought we could suggest that groups add material to the repo's wiki (they should have access) and this way presentations can be referenced after the course.

[sarahCobey]

I like it.

---

Sarah Cobey, PhD Assistant Professor Ecology & Evolution University of Chicago

(617) 756-7204 (cell) sarahcobey (Skype) cobeylab.uchicago.edu

On Sun, Jul 24, 2016 at 8:34 PM, Trevor Bedford notifications@github.com wrote:

Also, I thought we could suggest that groups add material to the repo's wiki (they should have access) and this way presentations can be referenced after the course.

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[trvrb]

That's 8 pathogens. We have 22 official registrants. We might get a couple drop ins, but this still nicely gives 3 people per group.

[trvrb]

Closing for 2016.