Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
Embrace me, surround me as the rush comes.Motorcycledrift deeper into the soundmore quotes

Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca
2020 `\pi` day art and the piku


visualization + design

“Transcendental Tree Map” from Yearning for the Infinite. This video premiered on 2020 Pi Day. Music by Max Cooper. Animation by Nick Cobby and myself.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 2020 Pi Day art celebrates digits of `\pi` with piku (パイク) —poetry inspired by haiku.
They serve as the form for The Outbreak Poems.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A `\pi` day music video!: Transcendental Tree Map premieres on 2020 Pi Day from Max Cooper's Yearning for the Infinite. Animation by Nick Cobby and myself. Watch live from Barbican Centre.

`\pi` Day 2020 Art — Digits, poetically.

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. I sympathize with this position and have `\tau` day art too!

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.
3 Little `\pi`,
1 what
4 can you tell us?

Welcome to this year's celebration of `\pi` and mathematics. Among the chaos of CORVID-19, this year `\pi` Day celebrations are short poetic emissions I call “piku” . They are brief pauses for the time.

Start by reading how piku are constructed and then browse submitted piku. Consider participating by submitting your own piku. All you need is a pen and a few (small) words. Very therapeutic.

But if the words here don't help, immerse yourself in my coronavirus art. It's quite catching.

If you enjoy poetry and words, see how I convert spam into poems in the style of ee cummings and if you like to see words arrange on page, look through my typographic art.

3 Piku are
1 brief
4 pauses just in
1 time.

You may know the haiku (俳句) as a short three line poem whose lines traditionally have 5, 7 and 5 syllables (specifically, morae or phonetic sounds).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Scribbles on Shonan Village Center notepad on which the idea was born. I am grateful for being invited to the Formalizing Biological and Medical Visualization (Shonan Meeting 167) in which the idea formed. (zoom)

On a recent trip to Japan I was looking to my environment for inspiration for this year's `\pi` Day. I also really wanted a scheme that would allow people to contribute to the art so that everyone could be both a participant and an audience.

After scribbling for a little bit (or a long while), I came up with the idea of a piku (`\pi`ku, パイク). Analogously to a haiku, the piku is poem whose structure is constrained. But in this case, the constraints are the digits of `\pi` itself.

The piku

The simplest piku is a 3 phrase poem with 3, 1 and 4 syllables, respectively. Perhaps the most trivial piku is just the list of digits.

3 Three one four
1 One
4 Five nine two six.

Specifically, Haiku count the number of phonetic sounds which isn't always the same as syllables. For example, the word "any" has two such sounds: a-ny.

If you're interested in how the counting of sounds is done in Japanese, read about marking time and beats in Haiku.

But a more fun one would be

3 A Three and
1 A
4 One and a four.

Longer words can be used, of course. But watch out for the lines that require a single syllable.

3 Numbers are
1 all
4 Equally fun.
3 Land meets sky.
1 Oh,
4 It's you again!

You can use hyphenation to work around the syllable count.

3 Memories
1 for-
4 get yourself then.

plural of piku is piku

Piku is singulare tantum—its plural form is the same as its singular.

This is because its inspiration is the haiku and in Japanese nouns do not have different singular and plural forms,

3 Piku is
1 the
4 piku plural.

Longer piku

In general, a piku may have more than 3 lines. This reflects the fact that the digits of `\pi` do not terminate.

3 Land meets sky.
1 Oh,
4 It's you again!
1 Yes,
5 Who did you expect?

The endless piku is just waiting to be written. Well... started, at least.

Handling zeros

The digit zero is a line with no syllables and corresponds to a compulsory verse break. But because the first zero in `\pi` is at digit 33, you wouldn't see a verse break for a while.

Therefore, you're free to introduce a verse break anywhere in the piku (this does not use up a digit). For example,

3 Hot air breeze
1 cools
4 much hotter things.

3 F 0 0
1 red
4 You add the light.

Generalizing the piku — the nku

Any number, `n`, has its own nku. The rules for its construction are the same: each digit generates a line with corresponding number of syllables.

For example, the haiku is an nku for `n = 575`.

The year of your birth has an nku—you might want to try composing one to reflect on your origins.

In fact, any date (e.g. DDMMYYYY) can be made into an nku. This year's `\pi` date in this format is 14032020 and here's one possible nku.

1 Dust
4 in space vacuum
0
3 clogs alien
2 machines.
0
2 Bummer.
0

The trailing zero in the number creates a verse break at the end of a poem. This can be ignored or used to generate a blank line if the poem is set with other text on the page.

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news + thoughts

The Outbreak Poems

Tue 24-03-2020

I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.

Thoughts crack through
night
to a still clock.
Clogged channels
stuck
with nervous silt.
Song to sleep
and
poem to wake
to.
Once in a
while
a long moment.
Lump on head
from
hole in stomach.
Universe 
of
no mind but ours.
Higher than
birds
stars glide at night.
Sleeps or hides
some
thing internal.
Pieces move by
rules
not yet written.
Clouds visit
then
as fog they stay.
Distant duck
bobs
like something else.
Not above
the
belows but in
them.
Yesterday
comes
by starlight to
day.
It's always
not
now somewhere else.

Read the poems and learn what a piku is.

Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses

Tue 17-03-2020

A poster full of epidemiological worry and statistics. Now updated with the genome of SARS-CoV-2 and COVID-19 case statistics as of 3 March 2020.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

Bacterial and viral genomes of various diseases are drawn as paths with color encoding local GC content and curvature encoding local repeat content. Position of the genome encodes prevalence and mortality rate.

The deadly genomes collection has been updated with a posters of the genomes of SARS-CoV-2, the novel coronavirus that causes COVID-19.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first SARS-CoV-2 genome (MT019529) to be sequenced appears first on the poster.

Using Circos in Galaxy Australia Workshop

Wed 04-03-2020

A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Using Circos in Galaxy Australia workshop. (zoom)

Download workshop slides.

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).

Essence of Data Visualization in Bioinformatics Webinar

Thu 20-02-2020

My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Essence of Data Visualization in Bioinformatics webinar. (zoom)

Download webinar slides.

Markov models — training and evaluation of hidden Markov models

Thu 20-02-2020

With one eye you are looking at the outside world, while with the other you are looking within yourself.
—Amedeo Modigliani

Following up with our Markov Chain column and Hidden Markov model column, this month we look at how Markov models are trained using the example of biased coin.

We introduce the concepts of forward and backward probabilities and explicitly show how they are calculated in the training process using the Baum-Welch algorithm. We also discuss the value of ensemble models and the use of pseudocounts for cases where rare observations are expected but not necessarily seen.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Markov models — training and evaluation of hidden Markov models. (read)

Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Markov models — training and evaluation of hidden Markov models. Nature Methods 17:121–122.

Background reading

Altman, N. & Krzywinski, M. (2019) Points of significance: Hidden Markov models. Nature Methods 16:795–796.

Altman, N. & Krzywinski, M. (2019) Points of significance: Markov Chains. Nature Methods 16:663–664.

Genome Sciences Center 20th Anniversary Clothing, Music, Drinks and Art

Tue 28-01-2020

Science. Timeliness. Respect.

Read about the design of the clothing, music, drinks and art for the Genome Sciences Center 20th Anniversary Celebration, held on 15 November 2019.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Luke and Mayia wearing limited edition volunteer t-shirts. The pattern reproduces the human genome with chromosomes as spirals. (zoom)

As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Precisely engineered frame mounts of flow cells used to sequence genomes in our laboratory. (zoom)

Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The plaque at the back of one of the framed Illumina flow cell. This one has sequence from a patient's lymph node diagnosed with Burkitt's lymphoma. (zoom)