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
In your hiding, you're alone. Kept your treasures with my bones.Coeur de Piratecrawl somewhere bettermore quotes

numbers: fun


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!

`\pi` Day 2017 Art Posters - Star charts and extinct animals and plants


Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / 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 Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2017 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` approximation day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2015 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` approx day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2013 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circular `\pi` art

On March 14th celebrate `\pi` Day. Hug `\pi`—find a way to do it.

For those who favour `\tau=2\pi` will have to postpone celebrations until July 26th. That's what you get for thinking that `\pi` is wrong.

If you're not into details, you may opt to party on July 22nd, which is `\pi` approximation day (`\pi` ≈ 22/7). It's 20% more accurate that the official `\pi` day!

Finally, if you believe that `\pi = 3`, you should read why `\pi` is not equal to 3.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
All art posters are available for purchase.
I take custom requests.

Caelum non animum mutant qui trans mare currunt.
—Horace

This year: creatures that don't exist, but once did, in the skies.

And a poem Of Black Body.

This year's `\pi` day song is Exploration by Karminsky Experience Inc. Why? Because "you never know what you'll find on an exploration".

If you like space, you'll love my the 12,000 billion light-year map of clusters, superclusters and voids. Find the biggest nothings in Boötes and Eridanus.

create myths and contribute!

Want to contribute to the mythology behind the constellations in the `\pi` in the sky? Many already have a story, but others still need one. Please submit your stories!

This year's `\pi` day art goes to space and there finds creatures that once called Earth home.

Well, I don't know if they called it home—at least a few thought it was a terribly inhospitable. All thought it was unforgivingly Darwinian.


Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Star chart of the first 12,000,000 digits of `\pi`. The 80 constellations honor extinct animals and plants. Azimuthal equidistant projection. (BUY ARTWORK)

the digits of `\pi` as a star catalogue

I asked the question: what happens if you interpret the digits of `\pi` as a catalogue of stars? What would the patterns in the sky look like? And, would they have stories? A couple of weeks later—and a few adventures down the rabbit holes of topographical projections—I found the answer.

The digits of Pi are interpreted as a star catalogue. Starting from the beginning of `\pi`, each block of 12 digits is taken to be the `(x, y, z)` coordinates of a star and its absolute magnitude, which defines its brightness at a fixed distance. After sampling 12 million digits, which yields 1,000,000 stars, the stars are projected onto the celestial sphere to generate longitude and latitude coordinates from the perspective of an observer who is placed at center of the stars. The distance to the star is used to calculate the apparent magnitude—how bright it will appear on the sky chart.


Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Star chart of the first 12,000,000 digits of `\pi`. The 80 constellations honor extinct animals and plants. Plate carrée projection. (BUY ARTWORK)

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Star chart of the first 12,000,000 digits of `\pi`. The 80 constellations honor extinct animals and plants. Hammer/Aitoff elliptical projection. (BUY ARTWORK)

Of course, a star chart would not be complete without constellations. While the digits of `\pi` are taken to be a universal catalog of stars, it is up to the observer to subjectively interpret the patterns and find stories in the sky. Among the 40,000 stars drawn in the chart, 80 extinct species are honored as constellations—creatures range across time periods and geographical location and play together in the sky. And much like the constellations that you might have seen in the real sky (the hunter Orion and winged-horse Pegasus) the `\pi` in the sky patterns represent creatures that do not exist.

The twist? They all once did!

chart variations

Charts are available in blue, black and white and sepia.


Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Star chart of the first 12,000,000 digits of `\pi`. The 80 constellations honor extinct animals and plants. Azimuthal equidistant projection. (BUY ARTWORK)

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Star chart of the first 12,000,000 digits of `\pi`. The 80 constellations honor extinct animals and plants. Azimuthal equidistant projection. (BUY ARTWORK)

poetry in the sky

This year's art is accompanied by a poem, Of Black Body, by Paolo Marcazzan. The poem is named after the idealized black body, an idealized material that absorbs all incident radiation.

There's plenty of nothing to see in space, Paolo insists, "there is nothing to see and you are seeing it. A truth that likes it here" and he hopes that you'll be find "drawn into our constellation, and cooling."

stories in the sky

There are indeed stories in the sky and many of them haven't yet been told. Below are just some of them.

More stories are available in the details about each constellation. There, for each animal you can find the common name, Latin name, when it was extinct and a link to Wikipedia to learn more about the animal. Many have stories which they would love to share with you.

raphus — egg guardian extraordinaire

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Raphus and Pecatonica

The Dodo bird (Raphus cucullatus) is vigilantly guarding his eggs—the clusters of stars just north of &alpha Raphus (the first brightest star in the constellation) and south of β Raphus (the second brightest star). He hardly seems to care about the pestering River Mayfly (Acanthometropus pecatonica), who is trying to draw his attention.

desmodus — nightly escape attempt

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Desmodus

Desmodus, the giant vampire bat (Desmodus draculae) is said to be trying to escape the dome of the sky each night. You might see his shape fluttering up into the top of the northern hemisphere.

basilosaurus — chasing the light in the deep

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Basilosaurus

The king lizard Basilosaurus (Basilosaurus cetoides) dives deeper and deeper at the bottom of the south hemisphere, as he chases the light of the bright magnitude 1.8 star α Basilosaurus, which sits at the very bottom of the chart.

quagga and aurochs — figuring out the stripes

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Quagga and Aurochs

There is plenty of land mass in teh north, where huge creatures like the mammoth (Mammuthus primigenius), sturdy aurochs (Bos primigenius) and the comical Quagga (Equus quagga quagga) run again. The Quagga cannot figure out his stripes and is seen frequently talking to the Aurochs, seeking his advice about the predicament of his patterns.

megalodon, rodhocetus and tecopa — the terror and the terrorized

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Megalodon, Rodhocetus and Tecopa

At the tip of the southern hemisphere drama unfolds as the monster shark Megalodon (Carcharodon megalodon) gives chase to the Tecopa pupfish (Cyprinodon nevadensis calidae) and Rodhocetus (Rodhocetus kasrani). Rodhocetus was an early whale that possessed land mammal characteristics and the story goes that he escaped Megalodon and lived out his life on the land, never returning to the sea.

camptor, mariana, alaotra and tadorna — I'm not a duck!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Camptor, Mariana, Alaotra and Tadorna

The south hemisphere also has plenty of calmer waters, where all manners of floating birds come for a swim and chat. These are represented by the triangular constellations of Camptor (Camptorhynchus labradorius, the Labrador duck), Alaotra grebe (Tachybaptus rufolavatus), Mariana mallard (Anas oustaleti) and the Korean crested shelduck (Tadorna cristata). Rumor has it Tadorna may have snuck into the sky without permission—while not seen since the 1960’s, some say the duck isn't actually extinct! Alaotra is frustrated that Tadorna seems to get all the attention. Often confused for a duck, Alaotra would love you to know that she's in fact a grebe. She's very proud of this fact, despite of being prone to falls due to some biomechanical issues having to do with foot placement.

yersinia — don't come close

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Yersinia

Don't let Yersinia's small size fool you. The Black Death (Yersinia pestis) may be the smallest creature in the sky, but she'll liquify your insides before you can memorize the 80 constellations. Perhaps out of all the creatures in the sky, this is the one we're happy to see go. But, because it's small, you can never be quite sure Yersinia isn't extinct but merely hiding. Or waiting.

pipilo — flocking across

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Pipilo

Pipilo is a rare flocking constellation and breaks the rule that a constellation should be a single connected component. Its stars are connected a loose pattern of pairs and show a flock of Bermuda towhees (Pipilo naufragus) crossing from the north to south hemispheres.

o'ahu 'akepa — two is such a lonely number

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
O'ahu 'akepa

Like Pipilo, the O'ahu 'akepa (Loxops wolstenholmei) is the only other multi-part constellation. Here, a pair of akepas are chatting and spreading rumors that Tadorna isn't actually extinct.

bron and compsognathus — big brothers and little friends

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Bron and Compsognathus

It's hard to be bigger than Bron (Brontosaurus excelsus), who must pay great attention not to step on his frolicking friend Compsognathus (Compsognathus longipes), who seeks to find protection in Bron's shadow. Some believe that if Bron stretches his neck, he can look above the sky!

pinta and cylindraspis — a friend for the end of the earth

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Pinta and Cylindraspis

Ever since Cylindraspis (Cylindraspis indica) heard that Pinta (Chelonoidis abingdonii) was the last of his kind, he decided to keep him company. They can be seen going for a very slow walk at the bottom of the sky, kept their by their heavy shells. The last Pinta—a turtle named Lonesome George—died in 2012.

xerces and Palaeoaldrovanda — flying flowers and hungry flowers

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Xerces and Palaeoaldrovanda

Xerces (Glaucopsyche xerces) is the only thing that is more brilliant than the blue sky itself. Some say that butterflies are flying flowers and Xerces is never seen far from Palaeoaldrovanda. He must be careful though. Rumor has it Palaeoaldrovanda was related to the carnivorous plant genus Aldrovanda! Nobody wants to take that chance.

araucaria — shelter for flying customers

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Araucaria

Xerces (Glaucopsyche xerces) is the only thing that is more brilliant than the blue sky itself. Some say that butterflies are flying flowers and Xerces is never seen far from Palaeoaldrovanda. He must be careful though. Rumor has it Palaeoaldrovanda was related to the carnivorous plant genus Aldrovanda! Nobody wants to take that chance.

araucaria — too large for the sky

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Araucaria

Araucaria (Araucaria mirabilis) is truly a marvel and it is too big to fit in the sky! The constellation only shows the canopy and does not include the tree trunk—which was known to reach a height of 100 m. Araucaria offers plenty of protection and has many flying friends all around, including Urania, Moho and WhĒkau. Just a little further are the ducks (and a grebe), Camptor, Mariana, Tadorna and Alaotra. They would love to visit Araucaria but worry that they are too heavy to perch on her branches.

ardea and aepyronis — who can see beyond the sky first?

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ardea and Aepyronis

The story goes that Camelops (Camelops kansansus) played a joke on Ardea (Ardea bennuides) and Aepyronis (Aepyornis maximus). He said "You both have long necks. But who has the longest? The first who can stretch far enough and tell me what is beyond the sky wins." To this day, Both Ardea and Aepyronis are seen straining their necks trying to win the bet.

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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.