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.
Survey of Hilbertonians
Below are some surveys that sample viable Hilbertonians. All of these Hilbertonians appear unique on the curve—they are all different with respect to rotation and flipping. Some of these have been turned into Hilbertonian posters, which you can buy.
To represent all of the 104,976 viable Hilbertonians we require that the lowest order curve on which they are drawn has at least 104,976 points.
An order 9 curve almost satisfies this requirement, with 49 = 262,144 points. So, if curves of order 9, 10 and 11 are used, they can enumerate the full set of viable Hilbertonians.
It's much easier to display all the shape-unique ones, of which there are 13,689.
To represent all 220 Hilbertonians, which includes the non-viable ones, we need to solve `4^n = 2^20` which gives `n=10`. So, if we draw curves of order 10, 11 and 12 we can show every possible Hilbertonian genome.
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news + thoughts
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 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.
Small hours of the world and me.
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses
A poster full of epidemiological worry and statistics. Now updated with the genome of SARS-CoV-2 and COVID-19 case statistics as of 3 March 2020.
Bacterial and viral genomes of various diseases are drawn as paths with color encoding local GC content and curvature encoding local repeat content. Position of the genome encodes prevalence and mortality rate.
The deadly genomes collection has been updated with a posters of the genomes of SARS-CoV-2, the novel coronavirus that causes COVID-19.
Using Circos in Galaxy Australia Workshop
A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.
Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).