resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
visualization + design
Hilbert Curve Art, Hilbertonians and Monkeys
I collaborated with Scientific American to create a data graphic for the September 2014 issue. The graphic compared the genomes of the Denisovan, bonobo, chimp and gorilla, showing how our own genomes are almost identical to the Denisovan and closer to that of the bonobo and chimp than the gorilla.
Here you'll find Hilbert curve art, a introduction to Hilbertonians, the creatures that live on the curve, an explanation of the Scientific American graphic and downloadable SVG/EPS Hilbert curve files.
Hilbertonians—creatures on the Hilbert Curve
Take a look at the Hilbertonian Posters and perhaps buy one. I take custom requests.
Hilbertonians: 101
Hilbertonians are creatures that live in the depths of the Hilbert curve. They live across three adjacent orders of the curve (e.g. 2, 3, 4). The come in many different personalities and many classes exist.
They are social—they always appear in multiples of 4. This is a consequence of how they are defined. A single Hilbertonian has never been seen.
Their genomes are 20 bases long. They only have 2 different types of bases. Out of a possible 220 = 1,048,576 genomes, only 104,976 (almost exactly 10%) produce living and breathing Hilbertonians, defined as those whose bodies form a contiguous shape. The other 943,600 are unfortunately unviable. The genomes of every Hilbertonian can be downloaded.
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news + thoughts
Poster Design Guidelines
Clear, concise, legible and compelling.
The PDF template is a poster about making posters. It provides design, typography and data visualiation tips with minimum fuss. Follow its advice until you have developed enough design sobriety and experience to know when to go your own way.
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.