resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
visualization + design
They serve as the form for The Outbreak Poems.
`\pi` Day 2014 Art Posters
On March 14th celebrate `\pi` Day. Hug `\pi`—find a way to do it.
For those who favour `\tau=2\pi` will have to postpone celebrations until July 26th. That's what you get for thinking that `\pi` is wrong. I sympathize with this position and have `\tau` day art too!
If you're not into details, you may opt to party on July 22nd, which is `\pi` approximation day (`\pi` ≈ 22/7). It's 20% more accurate that the official `\pi` day!
Finally, if you believe that `\pi = 3`, you should read why `\pi` is not equal to 3.
For the 2014 `\pi` day, two styles of posters are available: folded paths and frequency circles.
The folded paths show `\pi` on a path that maximizes adjacent prime digits and were created using a protein-folding algorithm.
The frequency circles colourfully depict the ratio of digits in groupings of 3 or 6. Oh, look, there's the Feynman Point!
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E=-23 of 64 digits of Pi, sorted by aspect ratio. Start (3) and end (2) digits are highlighted.
(zoom, BUY ARTWORK)
buy artwork
E=-23 of 64 digits of Pi, sorted by aspect ratio. Start (3) and end (2) digits are highlighted.
(zoom, BUY ARTWORK)
buy artwork
E=-23 of 64 digits of Pi, sorted by aspect ratio. Prime (2 3 5 7) digits are are highlighted.
(zoom, BUY ARTWORK)
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E=-23 of 64 digits of Pi, sorted by aspect ratio. Digits are colored by prime/composite status.
(zoom, BUY ARTWORK)
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E=-223 to -220 of 768 digits of Pi, sorted by aspect ratio. Start (3) and end (999999) digits are highlighted.
(zoom, BUY ARTWORK)
buy artwork
E=-223 to -220 of 768 digits of Pi, sorted by aspect ratio.. Start (3) and end (999999) digits are highlighted.
(zoom, BUY ARTWORK)
buy artwork
E=-223 to -220 of 768 digits of Pi, sorted by aspect ratio.. Prime (2 3 5 7) digits are are highlighted.
(zoom, BUY ARTWORK)
buy artwork
E=-223 to -220 of 768 digits of Pi, sorted by aspect ratio. Digits are colored by prime/composite status.
(zoom, BUY ARTWORK)
E=-223 to -209 of 768 digits of Pi, sorted by distance between start and end points (2.2–7.0). Start (3) and end (999999) digits are highlighted.
(zoom)
E=-223 of 768 digits of Pi. Start (3) and end (999999) digits are highlighted, as well as all prime digits. This path took about 1 CPU year to find. (37x51, r=0.725, area=1887, cm=1.9/13.4, dend=24.4)
(zoom)
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news + thoughts
The SEIRS model for infectious disease dynamics
Realistic models of epidemics account for latency, loss of immunity, births and deaths.
We continue with our discussion about epidemic models and show how births, deaths and loss of immunity can create epidemic waves—a periodic fluctuation in the fraction of population that is infected.
This column has an interactive supplemental component (download code) that allows you to explore epidemic waves and introduces the idea of the phase plane, a compact way to understand the evolution of an epidemic over its entire course.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.
Background reading
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.
Gene Machines
Shifting soundscapes, textures and rhythmic loops produced by laboratory machines.
In commemoration of the 20th anniversary of Canada's Michael Smith Genome Sciences Centre, Segue was commissioned to create an original composition based on audio recordings from the GSC's laboratory equipment, robots and computers—to make “music” from the noise they produce.
Virus Mutations Reveal How COVID-19 Really Spread
Genetic sequences of the coronavirus tell story of when the virus arrived in each country and where it came from.
Our graphic in Scientific American's Graphic Science section in the June 2020 issue shows a phylogenetic tree based on a snapshot of the data model from Nextstrain as of 31 March 2020.
Cover of Nature Cancer April 2020
Our design on the cover of Nature Cancer's April 2020 issue shows mutation spectra of patients from the POG570 cohort of 570 individuals with advanced metastatic cancer.
The cover design accompanies our report in the issue Pleasance, E., Titmuss, E., Williamson, L. et al. (2020) Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer 1:452–468.
Modeling infectious epidemics
Every day sadder and sadder news of its increase. In the City died this week 7496; and of them, 6102 of the plague. But it is feared that the true number of the dead this week is near 10,000 ....
—Samuel Pepys, 1665
This month, we begin a series of columns on epidemiological models. We start with the basic SIR model, which models the spread of an infection between three groups in a population: susceptible, infected and recovered.
We discuss conditions under which an outbreak occurs, estimates of spread characteristics and the effects that mitigation can play on disease trajectories. We show the trends that arise when "flattenting the curve" by decreasing `R_0`.
This column has an interactive supplemental component (download code) that allows you to explore how the model curves change with parameters such as infectious period, basic reproduction number and vaccination level.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.
The Outbreak Poems
I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.
Tears decline the plural of sad.
Souls look out from dark eye windows.