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Fred Hutch's List of science papers to read about the coronavirus

Fred Hutchinson Cancer Research Center's list of science papers you should be reading about the coronavirus: Amid the thousands of research publications on COVID-19, here are the ones they are reading

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Kristine Grayson onto COVID-19/Public Health

SEIR on networks with Github and Tweet thread

This is a python package for exploring SEIR models on social networks. The first link is to a Twitter thread where the use and some significant results are explained.

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Dr. Kestler’s Coronavirus Video Series

Dr. Harry Kestler at LCCC keeps us informed about the coronavirus and how we can all work together to slow the spread of COVID-19 in this series of daily videos about various aspects of the pandemic: https://www.lorainccc.edu/security/dr-kestlers-coronavirus-video-series/

Prior to his position at LCCC, Kestler held faculty positions at the Lerner Medical College of the Cleveland Clinic and the department of Microbiology and Molecular Genetics at Harvard Medical School.

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The mathematics of COVID-19

By Dr  Kamuela Yong

Helps readers interpret various models and statistics around COVID-19. Written at the introductory level, could be used for high school or introductory undergraduate.

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COVID 19 Data Pack

Several graphics around COVID19 and the pandemic, with readings at the bottom of the page and access to underlying data.

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Multiple R Shiny Dashboards tracking COVID-19

There is an R Shiny contest going on right now.  Many of the most recent submissions are data dashboards for tracking the COVID-19 pandemic.  Take a look!

 

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GISAID -Genomic epidemiology of hCoV-19

This phylogeny shows evolutionary relationships of hCoV-19 (or SARS-CoV-2) viruses from the ongoing novel coronavirus COVID-19 pandemic. This phylogeny shows an initial emergence in Wuhan, China, in Nov-Dec 2019 followed by sustained human-to-human transmission leading to sampled infections. Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred transmission patterns are only a hypothesis.

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SIR Model

This ESTEEM worksheet implements an SIR (Susceptible/ Infected/ Resistant) model of epidemiology for vector-borne diseases. Up to three microbial strains with different virulence and transmission parameters can be modeled and the results graphed. Originally designed to explore coevolution of myxoma and rabbits, the model is easily generalized to other systems.

The SIR Build It REVISED 2018 file attached here represents a basic SIR model and demonstrates Farr's law as well as the corresponding S/I phase plot. Additional sheets demonstrate some modifications of the basic model, including the effects of stochasticity.

From Tony Weisstein, Truman State

More Excel based simulations from the BioQUEST ESTEEM collection are available here:https://qubeshub.org/community/groups/esteem/esteem_modules_and_descriptions

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Calculus worksheet/questions for Flattening the Curve

For use in a calculus class!

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Khan Academy's COVID 19 estimations

Estimating actual COVID 19 cases (novel corona virus infections) in an area based on deaths. Based on work by Tomas Pueyo at: https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

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COVID 19 example of exponential growth, logistic curves and inflection points

From 3Blue1Brown animated math collection: https://www.3blue1brown.com/

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SEIR Shiny app

Doesn't require any simulator tools/R code. Just have your students play and look for insights!

Click on the intervention tab to see the #flattenthecurve app.

 

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Mathematics of the Corona outbreak – with professor Tom Britton

36 minute video on Youtube

"Many scientists try to predict the future and decide upon what preventive measures to take in order to mitigate the spread of the Covid-19 infection. But what is R_0 and how do you estimate it? What about #flattenthecurve? How does the math behind all this work and what does the statistical models look like? In this talk professor Britton explains all this."

 

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COVID-19 Data Set

From the description on Kaggle

"Johns Hopkins University has made an excellent dashboard using the affected cases data. Data is extracted from the google sheets associated and made available here.

Edited:
Now data is available as csv files in the Johns Hopkins Github repository. Please refer to the github repository for the Terms of Use details. Uploading it here for using it in Kaggle kernels and getting insights from the broader DS community."

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SEIR Worksheet in R

This is a relatively quick activity. A few lines of code utilizing the EpiDynamics R package gives students access to simulations of SEIR curves and can explore how lowering transmission rate helps flatten the curve. OER activity - fork it to add your own twist!

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Washington Post spatial simulation of social distancing

This is a Washington Post spatially-explicit simulation showing how social distancing helps flatten the curve and reduce overall infections.

General audience

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Gapminder

A fantastic tool for exploring public health, data, and data visualization.  The link will take you to teaching materials, but consider using the videos to prompt question exploration in the tools section.

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Kristin Jenkins onto COVID-19/Public Health

Genomic epidemiology of novel coronavirus (hCoV-19)

Data, figures and materials to explore.  No educational materials included.

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Kristin Jenkins onto COVID-19/Public Health