Meetup - ecology in Julia

[mkborregaard]

@tpoisot @richardreeve @kescobo I'm currently planning the "VizCon" in Berlin, the second installment of a meeting to advance plotting (and networking) in Julia. Last time it was really successful.

I was thinking, maybe we could all really benefit from doing a 1-week meetup/hackathon to talk and code and get ecology in Julia to a place where it's well-integrated and generally useful? I wouldn't mind coming to Montreal for a week at some point after the summer, which should also be really convenient for Kevin (and Richard loves travelling :smile: ).

What do you say?

[mkborregaard]

Sat to Sat then :-)

[kescobo]

Well, it's not for sure... God I'm a pain in the ass 😆

[richardreeve]

Not wishing to sound negative, but having come back from northern Italy last week to 2 weeks in isolation (one week to go, even though I have tested negative for coronavirus, because I have a cough!), I'm beginning to wonder exactly how wise it is to plan for a visit anywhere at the moment... I'm supposed to be on at least 5 more international trips this year including Montreal, but I'm struggling to believe they are all (any of them?) going to happen, and I'm certainly not booking any of them just yet...

[mkborregaard]

Shit. What were you doing in North Italy? Glad to hear you tested negative.

[richardreeve]

I was on long-booked holiday skiing! It was great, but the whole "save the planet by taking a train through England, France and Italy instead of flying" turned out to be a bit misjudged! To be honest, at this point I'd have been happy to get infected, so I could deal with it while we still had a functioning health care system...

[tpoisot]

In case the in-person meeting doesn't happen, we can (i) gather the local folks in a room large enough to maintain a 2m distance (probably), and then use a combo of zoom and teletype to work remotely.

[kescobo]

I suspect things will be much calmer by end of summer. Possibly gearing up for the next flu/corona season.

Or else civilization will have collapsed and nothing will matter.

[mkborregaard]

I still plan to come - as Kevin says it's likely to dissipate by May then launch a new attach next November, if it acts like any other temperate virus. I'm fine with waiting a bit with booking the tickets, and I definitely think we'll make most progress if Richard joins, but I'd most likely want to come anyway, if the rest of you are game.

[mkborregaard]

I guess @richardreeve really is the virologist here though. Isn't your key research area influenza virus?

[richardreeve]

Yes, we just published a PNAS paper on epidemiological and ecological interferences between flu (A and B), the common cold (rhinovirus) and other viruses, but sadly not coronaviruses, otherwise I guess my career would now be made! And we've just finished the vaccine selection for N Hemisphere winter flu vaccines, which will now take 8 months to manufacture... it'll be a while - this time next year at the earliest I guess - before we have any hope of a coronavirus vaccine. The good news is that the public health measures being brought in in Asia have stamped on the flu season - in some countries worst affected it's already ended 2 months early!

As far as Sept is concerned though, I just don't think we have enough data. I certainly don't know anything about its seasonality - if it survives better in the summer, that won't be ideal(!). If worse, then you're right, Sept may be too soon for a second wave. If it's pretty insensitive to climate, then it'll all depend on how effective our public health measures are - if they're utterly useless, then the worst may be over by Sept, but whether there'll be enough public infrastructure left in N America to host a meeting is probably in question. If they're averagely good, we could drag out the epidemic wave for months (which is good, we can keep hospitals functioning). If they're fantastic (à la Singapore), and I've seen no evidence they will be (though they did a good job with me to be fair), then maybe we'll have squashed this outbreak by then, so we'll be waiting for a second wave again...

Anyway, I don't have any more information than anyone else, so certainly don't believe anything I say here, but I'd just suggest not making any firm plans yet. For instance, my university could very plausibly impose a blanket ban on travel almost irrespective of the severity of the situation to protect our ability to function in the new academic year starting mid-Sept. I believe one of the virology labs I collaborate with have already done that to protect themselves.

Who knows, fundamentally?

PS "estimates of the overall case fatality rate in all infections (asymptomatic or symptomatic) of approximately 1%" (vs observed of >3%, means we're missing most cases in known infection chains); "two thirds of COVID-19 cases exported from mainland China have remained undetected worldwide" (v large numbers of wholly unknown infection chains being missed); "epidemic doubling time of approximately seven days" (growing fast); "on average, each case infected 2.6 (uncertainty range: 1.5-3.5) other people" (need to drop our infectiousness by >60% to stop a local outbreak).

[richardreeve]

That was a bit longer than I'd planned, sorry... tl;dr I think you're probably right that Sept may be a window of opportunity, but who knows!

[tpoisot]

Hi all - let's revive this discussion, do we want to have online sprint instead? It's clear there will be no travel in September, but we can most likely get things done remotely.

[mkborregaard]

Great idea. Yes, I'm all for that.

[richardreeve]

We're in a bit of an odd situation - we're currently using our spatial model as a COVID-19 model for the UK. Sadly, there are too few Julia programmers out there to spend time on our day jobs, much less anything else. Invenia are being very helpful, but if it's still ongoing in September (and it may well be obviously) then this won't be an option. If things have all settled down, then it would be great, but otherwise it'll be impossible to be honest.

[kescobo]

I've been meaning to revisit but was still holding out some totally unjustified hope. I think you're right. I'm in for online sprint.

@richardreeve Totally understandable - perhaps we can do a bit more up-front planning so that you can chime in on design decisions and then the rest of us can push ahead with a bit more confidence that we can get everything to work together in the end.

Also tagging @pdimens, author of https://github.com/pdimens/PopGen.jl, since I think he would make a valuable addition (and integrating population genetics with all of the ecology tooling would be just amazing, I think).

[pdimens]

I'm all for incorporation of PopGen.jl into EcoJulia, and would be interested in chatting with someone that can help me understand how to do that.

[tpoisot]

@richardreeve fully understandable and I agree with @kescobo idea of agreeing on implementation -- having @pdimens onboard is also fantastic! Do we feel like a quick zoom is justified at this point? I know that at least @FrancisBanville and @gabrieldansereau will attend JuliaCon virtually to talk about their ecological use cases, so they might have some additional comments (and pain points they identified).

[mkborregaard]

Quick zoom sounds good. Is everyone online at this point?

[kescobo]

I'm UTC-4 (US east coast) and available most days ~9am-4pm

[pdimens]

Same as @kescobo -1

[FrancisBanville]

Yes, I agree that a quick Zoom call can be helpful!

I will be available as of August 10th, almost at any time during the day.

[tpoisot]

Same as Francis

Sent from Outlook Mobilehttps://aka.ms/blhgte

---

From: Francis Banville notifications@github.com Sent: Thursday, July 30, 2020 6:10:29 PM To: EcoJulia/SpatialEcology.jl SpatialEcology.jl@noreply.github.com Cc: Poisot Timothée timothee.poisot@umontreal.ca; Mention mention@noreply.github.com Subject: Re: [EcoJulia/SpatialEcology.jl] Meetup - ecology in Julia (#49)

Yes, I agree that a quick Zoom call can be helpful!

I will be available as of August 10th, almost at any time during the day.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/EcoJulia/SpatialEcology.jl/issues/49#issuecomment-666736540, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAENOAJVYM4ADRM4HXIM2B3R6HVVLANCNFSM4KQJKQ5A.

[kescobo]

Alright, just to move things along, I'm going to propose next Tuesday Aug 11, UTC 15:00.

Going to post zoom details on slack in #ecology channel, shoot me an e-mail (there's an address on my GH profile) or DM on Discourse if you're not using slack.

[tpoisot]

Do you mean #ecojulia? I don't see an #ecology channel on the main slack. Should we setup a gitter?

[kescobo]

I've set up an ecology zulip stream for more persistent conversation.

From slack discussion - we'll meet today as I proposed, but will take notes on what's discussed, and do not expect anything to be the final word. If you can't make it, don't hesitate to chime in after the fact!

Wondering about collaborative document editing - I can set up a google doc, but I'm open to other tools. Regardless, I'll write it all up formatted for github and post here.