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.
download art files
Vector art files of Hilbert curves of order 1 to 10. Each curve is a path in its own layer.
The figure below shows what the files contain, except the figure has different stroke and transparency settings for each order. In the downloadable files, each order's thickness and color is the same.
square
Download Hilbert curve in PDF EPS AI format.
circular
The mapping of the Hilbert curve onto a circle was done using this transformation
`[x',y'] = [x\sqrt{1-y^2/2},y\sqrt{1-x^2/2}]`
which maps the region ` -1 <= x <1, -1 <= y < 1` onto the circle at ` (x,y,r)=(0,0,1) `. I've used this before to transform folded paths of the digits of `\pi`. This transformation is described in detail here.
Download Hilbert curve mapped onto a circle in PDF EPS AI format.
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news + thoughts
Points of Significance celebrates 50th column
We are celebrating the publication of our 50th column!
To all our coauthors — thank you and see you in the next column!
Uncertainty and the management of epidemics
When modelling epidemics, some uncertainties matter more than others.
Public health policy is always hampered by uncertainty. During a novel outbreak, nearly everything will be uncertain: the mode of transmission, the duration and population variability of latency, infection and protective immunity and, critically, whether the outbreak will fade out or turn into a major epidemic.
The uncertainty may be structural (which model?), parametric (what is `R_0`?), and/or operational (how well do masks work?).
This month, we continue our exploration of epidemiological models and look at how uncertainty affects forecasts of disease dynamics and optimization of intervention strategies.
We show how the impact of the uncertainty on any choice in strategy can be expressed using the Expected Value of Perfect Information (EVPI), which is the potential improvement in outcomes that could be obtained if the uncertainty is resolved before making a decision on the intervention strategy. In other words, by how much could we potentially increase effectiveness of our choice (e.g. lowering total disease burden) if we knew which model best reflects reality?
This column has an interactive supplemental component (download code) that allows you to explore the impact of uncertainty in `R_0` and immunity duration on timing and size of epidemic waves and the total burden of the outbreak and calculate EVPI for various outbreak models and scenarios.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Uncertainty and the management of epidemics. Nature Methods 17.
Background reading
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.
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.
Cover of Nature Genetics August 2020
Our design on the cover of Nature Genetics's August 2020 issue is “Dichotomy of Chromatin in Color” . Thanks to Dr. Andy Mungall for suggesting this terrific title.
The cover design accompanies our report in the issue Gagliardi, A., Porter, V.L., Zong, Z. et al. (2020) Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes. Nature Genetics 52:800–810.
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.
