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#sirmodel#epidemicsimulation#3blue1brown

Simulating an epidemic

3Blue1Brown

8.7M subscribers • 42 videos on Hallway

YouTube
  • Recommended by 8 people: 8 on Hacker News.
  • Presented by Grant Sanderson, creator of 3Blue1Brown
  • Linked in the description3b1b/manim3b1b/videos

Beginner. No background in the topic needed.

5.2M views6 years ago8 recommendations

Computer scienceGraphics and audioAlgorithmsData visualizationMath for programmers

Grant Sanderson uses toy SIR models to simulate how epidemics spread and visualizes the effects of various intervention strategies.

Experiments with toy SIR models Help fund future projects: patreon.com/3blue1brown An equally valuable form of support is to simply share some of the videos. Special thanks to these supporters: 3b1b.co/sir-thanks Home page: 3blue1brown.com Awesome fan-made interactives: prajwalsouza.github.io/Experiments/Epidemic-Simulation.html learningsim.itch.io/pandemic-spread-simulation Simulations by Harry Stevens at the Washington Post: washingtonpost.com/graphics/2020/world/corona-simulator/ Simulations by Kevin Simler at Melting Asphalt: meltingasphalt.com/interactive/outbreak/ Excellent visualization of each country's current growth from Minutephysics and Aatish Bhatia: youtube.com/watch?v=54XLXg4fYsc Another good interactive to see what effect various parameters have on the shape of the curve: gabgoh.github.io/COVID/index.html If you want to hear a mathematician/epidemiologist's summary of COVID-19, I found this MSRI talk very worthwhile: youtu.be/MZ957qhzcjI Marcel Salathé on Contact Tracing: twitter.com/marcelsalathe/status/1242430736944201730 Thanks to these viewers for their contributions to translations Hebrew: Omer Tuchfeld ------------------ These animations are made using manim, a scrappy open-source python library: github.com/3b1b/manim Code for this video: github.com/3b1b/videos/blob/master/_2020/sir.py Honestly, given that the code for that video is meant for demo purposes, and not meant to reflect the true data of COVID-19, if you want to apply these ideas to the current situation I'd recommend looking for more professional epidemiological modeling tools that are less centered around animations and pedagogy and more focused on accurate predictions. For example, the Institute for Disease Modeling has a lot of models free for people to look at and play with. --------------- Opening music: Candlepower by Chris Zabriskie is licensed under a Creative Commons Attribution license (creativecommons.org/licenses/by/4.0/) Source: chriszabriskie.com/divider/ Artist: chriszabriskie.com/ Other music by Vincent Rubinetti. Download the music on Bandcamp: vincerubinetti.bandcamp.com/album/the-music-of-3blue1brown Stream the music on Spotify: open.spotify.com/album/1dVyjwS8FBqXhRunaG5W5u If you want to contribute translated subtitles or to help review those that have already been made by others and need approval, you can click the gear icon in the video and go to subtitles/cc, then "add subtitles/cc". I really appreciate those who do this, as it helps make the lessons accessible to more people. ------------------ 3blue1brown is a channel about animating math, in all senses of the word animate. And you know the drill with YouTube, if you want to stay posted on new videos, subscribe: 3b1b.co/subscribe Various social media stuffs: Website: 3blue1

Why it's here

8 people recommend this

What people say. Recommended as an exceptionally clear and digestible visual explanation of epidemic modeling and SIR simulations.

foobarbecueon Hacker News • Recommends

On “Japan set to ban entry from the U.S. as early as next week”

Part of 3 Blue 1 Brown's excellent latest video simulates travel restrictions and suggests they're not very effective: link to this video . However, that was only for cutting travel between all communities by a factor of 4, rather than completely banning travel between two particular communities / countries.

kauntaon Hacker News • Recommends

On “Building a command line tool to simulate the spread of an infection”

Garrett, thank you. * * * My inspiration for writing this came from watching 3Blue1Brown's YouTube video, "Simulating an epidemic": link to this video His simulations cover several scenarios: - Simulating social distancing. - Having people travel to a central location (e.g. a grocery store). - What if the government is able to identify and isolate cases? - Simulating multiple communities with travel, that put quarantine measures in place. - What happens when people get tired of social distancing. * * * Thanks for sharing your code. I see that you are using gnuplot to visualize the output of the script. Have you considered using the csv module ( link ) to output the data, instead of using the print()…

gilbetronon Hacker News • Recommends

On “FDA grants emergency use authorization for 5-13 minute Covid-19 test”

If we can test and isolate, we can manage how the disease progresses through society, with a (very very slight, now) chance of stopping it. While not scientific, this is illustrative and well done that shows many aspects of disease spread: link to this video

mcsb4on Hacker News • Recommends

On “Austria to make basic face masks compulsory in supermarkets”

…until we either have a vaccine or ~60% of the population have antibodies. So the choice is to sit the next 12-18months at home or we fight the transmission of the virus. Masks cost nothing compared to the economic disaster that we are running into. The virus spreads via mouth and nose and secondary via the hands. So just stop it at the source. 1 link to this video…

ignoramouson Hacker News • Recommends

On “Covid-19 Antibody Seroprevalence in Santa Clara County, California”

> ...noticeable reduction in the spread? I believe the SIR model 0 answers those questions. 3blue1brown's video on the topic is super digestible and informative 1. In short, the discovery of a prophylactic if not a therapeutic treatment are our best immediate bets, absent which, quarantines and lockdowns will have to persist to curb the spread of a disease as infectious as covid-19 whilst we patiently wait for an effective vaccine against it 2. 0 link 1 link to this video 2 link

tmabrahamon Hacker News • Recommends

On “Manim: Animation engine for explanatory math videos”

BTW, he's currently co-teaching a course on Julia with some really great lectures on computational thinking: link He also had a nice video about epidemics/pandemics: link to this video All using manim for visualizations.

gus_massaon Hacker News • Recommends

On “Contra Weyl on Technocracy”

…one meets everyone randomly. It's more complicated if you want to consider a more realistic model of how people move. For a decision about lockdown you need the complex model, but to understand herd immunity the simple model is good enough. For a nice explanation of more complicated models, there is a video of 3Blue1Brown: "Simulating an epidemic" link to this video Note that he explains that the models in this video are not 100% accurate, some number are chosen to get nice graphics, they are only useful to get some insight but not get quantitative predictions.…

systemvoltageon Hacker News • Recommends

On “India’s second wave of Covid-19 feels nothing like its first”

Dynamics of the virus spread is quite interesting. 3Blue1Brown made a fascinating video about how an epidemic spreads: link to this video

CHsurferon Hacker News • Mentions

On “Austria to make basic face masks compulsory in supermarkets”

This seems like such a no-brainer. 3Blue 1Brown did a video on epidemic simulation, and central markets, places where people in the region congregate, are major factors in the the rate of disease spread. Limiting the transfer coefficient in these places has the key to reducing this impact, assuming you can't prevent people from going there. link to this video

michaelton Hacker News • Mentions

On “We’re working on 1M Covid-19 testing capacity per day”

Basically, some simulations show 1 if lots of people from an otherwise-socially-distancing population all go to one central location, that increases the R0 (i.e. spread) of the virus. This is a problem for anything that draws together lots of people from a large area into the same place - trade shows, sports events, music festivals, cinemas, conventions, busses and trains, food stores, beaches, universities and schools. We almost certainly haven't hit on the most optimal solution - in my country we closed schools, yet keeping crowded metro trains running? - but it wouldn't have been wise to wait for more data to come in before taking any action. 1 link to this video

salimmadjdon Hacker News • Mentions

On “The epidemiologist behind Sweden’s controversial coronavirus strategy”

…ne counter point by Johan Giesecke was that these flattening the curve is motivated by the assumption of a static capacity of ER rooms to deal with this pandemic and he pointed out they have increased capacity. Overall I found listening to his side very informative, at least it gave me a different view of looking at from their view. 0 link 1 link to this video…

shawnzon Hacker News • Mentions

On “A Third Solution”

> screening everyone every day (which is very different from simply doing "more testing"). That seems like the logical conclusion of "more testing" to me. If we could, why wouldn't we? 3blue1brown on YouTube did an analysis which similarly shows that fast quarantining is the best way to mitigate the virus: link to this video

thu2111on Hacker News • Mentions

On “Flatten the Curve of Armchair Epidemiology”

It's pretty apparent the writers don't understand epidemiology themselves. What is this field, really? It's not medicine. Its most famous practitioners often don't have any medical training or background, e.g. Prof Ferguson who did his PhD in theoretical physics. The assumptions it uses are of the level of medical complexity that a small child can understand - essentially that people who spend time close to each other infect each other. The models don't take as input the molecular biology or DNA of a virus that's being simulated. Arguably it's not science. A basic characteristic of science is that it tells us something new about the world, something that can be proven true. Experiments are f…

ilogikon Hacker News • Mentions

On “Why SARS-CoV-2 Bluetooth contact tracing apps are a tremendously stupid idea”

the whole point of the app is to isolate people that have been in contact with positive cases before they become contagious. if everyone has the app, you won't have an exponential growth. link to this video

andreareinaon Hacker News • Mentions

On “What's the point of a Covid-19 test that takes 19 days for results?”

Not exactly a citation1, but this agent-based simulation suggest that mitigations like quarantine are highly sensitive to how thoroughly they are applied: link to this video 1 I'm putting this firmly in the "all models are wrong, but some models are useful" camp

leobgon Hacker News • Mentions

On “Did lockdowns work? The verdict on Covid restrictions”

I don’t get it. How can social distancing NOT help during a pandemic? Quote from the book 1491: “One reason is that Indians were fresh territory for many plagues, not just one. Smallpox, typhoid, bubonic plague, influenza, mumps, measles, whooping cough—all rained down on the Americas in the century after Columbus. (Cholera, malaria, and scarlet fever came later.) Having little experience with epidemic diseases, Indians had no knowledge of how to combat them. In contrast, Europeans were well versed in the brutal logic of quarantine. They boarded up houses in which plague appeared and fled to the countryside.” And here’s 3Blue1Brown running a simulation: link to this video