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.
news + thoughts
Oryza longistaminata genome cake
Data visualization should be informative and, where possible, tasty.
Stefan Reuscher from Bioscience and Biotechnology Center at Nagoya University celebrates a publication with a Circos cake.
The cake shows an overview of a de-novo assembled genome of a wild rice species Oryza longistaminata.
Optimal experimental design
Customize the experiment for the setting instead of adjusting the setting to fit a classical design.The presence of constraints in experiments, such as sample size restrictions, awkward blocking or disallowed treatment combinations may make using classical designs very difficult or impossible.
Optimal design is a powerful, general purpose alternative for high quality, statistically grounded designs under nonstandard conditions.
We discuss two types of optimal designs (D-optimal and I-optimal) and show how it can be applied to a scenario with sample size and blocking constraints.
Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design Nature Methods 15:599–600.
Background reading
Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.
Krzywinski, M. & Altman, N. (2014) Points of significance: Analysis of variance (ANOVA) and blocking. Nature Methods 11:699–700.
Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments. Nature Methods 11:597–598.
The Whole Earth Cataloguer
All the living things.An illustration of the Tree of Life, showing some of the key branches.
The tree is drawn as a DNA double helix, with bases colored to encode ribosomal RNA genes from various organisms on the tree.
All living things on earth descended from a single organism called LUCA (last universal common ancestor) and inherited LUCA’s genetic code for basic biological functions, such as translating DNA and creating proteins. Constant genetic mutations shuffled and altered this inheritance and added new genetic material—a process that created the diversity of life we see today. The “tree of life” organizes all organisms based on the extent of shuffling and alteration between them. The full tree has millions of branches and every living organism has its own place at one of the leaves in the tree. The simplified tree shown here depicts all three kingdoms of life: bacteria, archaebacteria and eukaryota. For some organisms a grey bar shows when they first appeared in the tree in millions of years (Ma). The double helix winding around the tree encodes highly conserved ribosomal RNA genes from various organisms.
Johnson, H.L. (2018) The Whole Earth Cataloguer, Sactown, Jun/Jul, p. 89
Why we can't give up this odd way of typing
All fingers report to home row.An article about keyboard layouts and the history and persistence of QWERTY.
My Carpalx keyboard optimization software is mentioned along with my World's Most Difficult Layout: TNWMLC. True typing hell.
McDonald, T. (2018) Why we can't give up this odd way of typing, BBC, 25 May 2018.
Molecular Case Studies Cover
The theme of the April issue of Molecular Case Studies is precision oncogenomics. We have three papers in the issue based on work done in our Personalized Oncogenomics Program (POG).
The covers of Molecular Case Studies typically show microscopy images, with some shown in a more abstract fashion. There's also the occasional Circos plot.
I've previously taken a more fine-art approach to cover design, such for those of Nature, Genome Research and Trends in Genetics. I've used microscopy images to create a cover for PNAS—the one that made biology look like astrophysics—and thought that this is kind of material I'd start with for the MCS cover.
Happy 2018 `\tau` Day—Art for everyone
