Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
This love loves love. It's a strange love, strange love.Liz Fraserfind a way to lovemore quotes

In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 2018 Pi Day art celebrates the 30th anniversary of `\pi` day and connects friends stitching road maps from around the world. Pack a sandwich and let's go!

The art of Pi (`\pi`), Phi (`\phi`) and `e`


Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2018 `\pi` day shrinks the world and celebrates road trips by stitching streets from around the world together. In this version, we look at the boonies, burbs and boutique of `\pi` by drawing progressively denser patches of streets. Let's go places.

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2017 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` approximation day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2015 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` approx day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2013 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circular `\pi` art

Numbers are a lot of fun. They can start conversations—the interesting number paradox is a party favourite: every number must be interesting because the first number that wasn't would be very interesting! Of course, in the wrong company they can just as easily end conversations.

The art here is my attempt at transforming famous numbers in mathematics into pretty visual forms, start some of these conversations and awaken emotions for mathematics—other than dislike and confusion

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Like music with numbers? Try Angels at My Door (Una), Pt vs Ys (Yoshinori Sunahara), 2wicky (Hooverphonic), One (Aimee Mann), Straight to Number One (Touch and Go), 99 luftbaloons (Nena).

Numerology is bogus, but art based on numbers can be beautiful. Proclus got it right when he said (as quoted by M. Kline in Mathematical Thought from Ancient to Modern Times)

Wherever there is number, there is beauty.
Proclus Diadochus


Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
2,258 digits of `\phi`, 3,855 digits of `e` and 3,628 digits of `\pi` in 6 level treemaps. Uniform line thickness. Bauhaus prime colors in Piet Mondrian style. (2015 `\pi` day posters, BUY ARTWORK)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
All art posters are available for purchase.
I take custom requests.

the numbers π, φ and e

The consequence of the interesting number paradox is that all numbers are interesting. But some are more interesting than others—how Orwellian!

All animals are equal, but some animals are more equal than others.
—George Orwell (Animal Farm)

Numbers such as `\pi` (or `\tau` if you're a revolutionary), `\phi`, `e`, `i = \sqrt{-1}`, and `0` have captivated imagination. Chances are at least one of them appears in the next physics equation you come across.

π 
φ
e 
= 3.14159 26535 89793 23846 26433 83279 50288 41971 69399 ...
= 1.61803 39887 49894 84820 45868 34365 63811 77203 09179 ...
= 2.71828 18284 59045 23536 02874 71352 66249 77572 47093 ...

Of these three transcendental numbers, `\pi` (3.14159265...) is the most well known. It is the ratio of a circle's circumference to its diameter (`d = \pi r`) and appears in the formula for the area of the circle (`a = \pi r^2`).


Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
2,258 digits of `\phi`, 3,855 digits of `e` and 3,628 digits of `\pi` in 6 level treemaps. Uniform line thickness. Bauhaus prime colors in Piet Mondrian style. (2016 `\pi` day posters, BUY ARTWORK)

The Golden Ratio (`\phi`, 1.61803398...) is the attractive proportion of values `a > b` that satisfy `{a+b}/2 = a/b`, which solves to `a/b = {1 + \sqrt{5}}/2`.

The last of the three numbers, `e` (2.71828182...) is Euler's number and also known as the base of the natural logarithm. It, too, can be defined geometrically—it is the unique real number, `e`, for which the function `f(x) = e^x` has a tangent of slope 1 at `x=0`. Like `\pi`, `e` appears throughout mathematics. For example, `e` is central in the expression for the normal distribution as well as the definition of entropy. And if you've ever heard of someone talking about log plots ... well, there's `e` again!

Two of these numbers can be seen together in mathematics' most beautiful equation, the Euler identity: `e^{i\pi} = -1`. The tau-oists would argue that this is even prettier: `e^{i\tau} = 1`.

accidentally similar

Did you notice how the 13th digit of all three numbers is the same (9)? This accidental similarity generates its own number—the Accidental Similarity Number (ASN).

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news + thoughts

Predicting with confidence and tolerance

Wed 07-11-2018
I abhor averages. I like the individual case. —J.D. Brandeis.

We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.

Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Predicting with confidence and tolerance. (read)

Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.

Background reading

Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.

4-day Circos course

Wed 31-10-2018

A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Composite of the kinds of images you will learn to make in this course.

Oryza longistaminata genome cake

Mon 24-09-2018

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circos cake celebrating Reuscher et al. 2018 publication of the Oryza longistaminata genome.

Optimal experimental design

Tue 31-07-2018
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Optimal experimental design. (read)

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

Mon 30-07-2018
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The circle of life. (read, zoom)

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

Mon 30-07-2018
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
TNWMLC requires seriously flexible digits. It’s 87% more difficult than using a standard Qwerty keyboard, according to Martin Krzywinski, who created it (Credit: Ben Nelms). (read)

McDonald, T. (2018) Why we can't give up this odd way of typing, BBC, 25 May 2018.