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
And whatever I do will become forever what I've done.Wislawa Szymborskadon't rehearsemore quotes


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


art + design

Math geek? If you like the clean geometric design of the type posters, you may enjoy something even more mathematical. Design that transcends repetition: Art of Pi, Phi and e posters.

Visions of Type

typography and bird songs

Consider the fact that, if you live in a city, birds are essentially the only wildlife that you meet during your day.

Depending on where you live, you might come several species without even trying. In Vancouver, on my short 10 minute walk to work, I have a good chance to see rock doves, crows, mallars, wigeons, hooded mergansers (if I'm lucky), house sparrows, song sparrows, red-winged black birds, white-crowned sparrows, bushtits, black-capped chickadees, northern flickers, and the mother-of-all-honkers: Canada geese.

Birds and letters are everywhere—art of nature and man.

Letter forms, on the other hand, are the art that is also everywhere. Every typeface is an artistic expression.

Regardless where you live, sadly, you are likely to come across mutants like Comic Sans, Arial and Times New Roman. Hideous creatures from the shallows. Try to find Gotham, Gill Sans, Frutiger, or Garamond.

learning bird songs

Mnemonics of bird songs help you remember the call and recognize the bird. It's so much easier to think "Quick, three beers!" — the call of the Olive-sided flycatcher — rather than "Chirp, chirp, chirp."

The mnemonic captures the cadence and repetition scheme of the song.

For example, if you listen to the white-throated sparrow you can't help but think that this little guy is trying to tell us something.

the mnemonics

French Zonotrichia albicollis: Baisse ta jupe, Philomène, Philomène, Philomène. How differently we hear!
—Madelaine Lemieux (via Twitter)

Dear sweet Canada Canada Canada.
White-throated Sparrow (Zonotrichia albicollis)

Potato chip!
American Goldfinch (Spinus tristis)

Here here. Come right here, dear.
Baltimore Oriole (Icterus galbula)

Who cooks for you?
Barred Owl (Strix varia)

Fire fire. Where where? Here here! See it, see it.
Indigo Bunting (Passerina cyanea)

Clear. Wick, wick, wick.
Northern Flicker (Colaptes auratus)

Quick, three beers!
Olive-sided Flycatcher (Contopus cooperi)

Where are you? Here I am.
Red-eyed Vireo (Vireo olivaceus)

Chubby chubby cheeks. Chubby cheeks.
Ruby-crowned kinglet (Regulus calendula)

Here sweetie.
Black-capped chickadee (Poecile atricapillus)

See me, pretty, pretty me.
White-crowned sparrow (Zonotrichia leucophrys)

the posters

If you love birds and typography, these posters are for you.

The mnemonic for the bird's song is presented on a background that proportionally presents the bird's plumage colors.

If you explore the posters, you just might find the bird too.


Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Dear sweet Canada Canada Canada. — song of the White-throated Sparrow (Zonotrichia albicollis). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Potato chip! — song of the American Goldfinch (Spinus tristis). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Here here. Come right here, dear. — song of the Baltimore Oriole (Icterus galbula). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Who cooks for you? — song of the Barred Owl (Strix varia). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Fire fire. Where where? Here here! See it, see it. — song of the Indigo Bunting (Passerina cyanea). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Clear. Wick, wick, wick. — song of the Northern Flicker (Colaptes auratus). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Quick, three beers! — song of the Olive-sided Flycatcher (Contopus cooperi). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Where are you? Here I am. — song of the Red-eyed Vireo (Vireo olivaceus). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Chubby chubby cheeks. Chubby cheeks. — song of the Ruby-crowned kinglet (Regulus calendula). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Here sweetie. — song of the Black-capped chickadee (Poecile atricapillus). (BUY ARTWORK)

Typographical posters of bird song
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
See me, pretty, pretty me. — song of the White-crowned sparrow (Zonotrichia leucophrys). (BUY ARTWORK)
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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