Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
Thoughts rearrange, familiar now strange.Holly Golightly & The Greenhornes break flowersmore quotes

computing: recursive


The Outbreak Poems — artistic emissions in a pandemic


data visualization + art

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Like algorithms?
Enjoy even more `\\pi` art.

Hola Mundo and Hello `\pi`

Art is science in love.
— E.F. Weisslitz

Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Remix of the cover design of Hola Mundo by Hannah Fry. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Remix of the cover design of Hola Mundo by Hannah Fry. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Remix of the cover design of Hola Mundo by Hannah Fry. (zoom)

art and algorithms

Some algorithms connect us and some keep us apart—we need them to remind us what it is to be human and what it is to be a computer.

My cover design for Hannah Fry's Hello World: Being Human in the Age of Algorithms is based on my 2013 `\pi` Day art. The book is published by Blackie Books.

Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Published by Blackie Books. Cover design by Martin Krzywinski. The front cover of the book shows a network based on the first 1,418 digits of `\pi`. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Published by Blackie Books. Cover design by Martin Krzywinski. The back cover of the book shows a network based on the first 837 digits of `\pi`. (zoom)

creating the cover

The cover begins with a 57 × 35 matrix of 1,995 colored circles. Each circle encodes a digit of `\pi`, starting with 3.1415.... Inside each circle is a smaller circle whose color is based on the next digit. The radius of the inner circle is `1/\phi^2` where `1/\phi = 0.618` is the Golden Ratio.

Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The beginning of the cover design. 1,995 colored circles encode digits of `\pi`. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Each circle has a smaller circle inside it that encodes the next digit. (zoom)

Once the circles are drawn, neighbouring circles that correspond to the same digit are connected with thick lines. The thickness of these lines is `t_0 = 3/(2\phi^2)`, relative to the outer circle radius. Circles that correspond to digits whose difference is `1` or `-1` are connected by a slightly thinner line with thickness `t_1 = t_0/\phi`.

Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Neighbouring identical digits are connected with thick lines. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Neighbouring digits that are off by 1 are connected by thinner lines. (zoom)

More lines are drawn that connect digits with a larger difference, `|d| > 1`. The thickness for these lines is `t_d = t_0/\phi^{|d|}`. When all differences up to `|d| < 6` are accounted for, we get a pleasant jumble of lines.

Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Neighbouring digits whose difference is greater than one are connected by progressively thinner lines. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circles representing the digits of `\pi` with all lines connecting neighbouring digits. (zoom)

To accommodate the title and other text on the cover, the design was generated by avoiding drawing any circles within a certain distance of the text.

This way, the network of digits wraps around the text. In the final design, the front page has 1,418 digits and the back has 878 digits.

Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Cover design by Martin Krzywinski. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Cover design by Martin Krzywinski. (zoom)

cover remixes

just the lines

Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Just the connecting lines. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Triangle color is the average color of their corners. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Inner circles punched out. (zoom)
Cover design by Martin Krzywinski of Hola Mundo (Hannah Fry) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Just the triangles. (zoom)

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news + thoughts

The SEIRS model for infectious disease dynamics

Thu 18-06-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: The SEIRS model for infectious disease dynamics. (read)

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: The SEIRS model for infectious disease dynamics. (Interactive supplemental materials)

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

Fri 05-06-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Gene Machines by Segue. Now available on vinyl.

Virus Mutations Reveal How COVID-19 Really Spread

Mon 01-06-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Virus Mutations Reveal How COVID-19 Really Spread. Text by Mark Fischetti (Senior Editor), art direction by Jen Christiansen (Senior Graphics Editor), source: Nextstrain (enabled by data from GISAID).

Cover of Nature Cancer April 2020

Mon 27-04-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Each ellipse system represents the mutation spectrum of an individual patient. Individual ellipses in the system correspond to the number of base changes in a given class and are layered by mutation count. Ellipse angle is controlled by the proportion of mutations in a class within the sample and its size is determined by a sigmoid mapping of mutation count scaled within the layer. The opacity of each system represents the duration since the diagnosis of advanced disease. (read more)

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

Tue 16-06-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

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`.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

The Outbreak Poems

Sat 04-04-2020

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.

Read the poems and learn what a piku is.