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


outbreak + poetry

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.

The Outbreak Poems

Short emissions from piku actual during the coronavirus outbreak.

If you don't know how to feel about that, refer to my tree of emotional life.

The pikus are ordered by time, with the most recent first. Learn about piku.

Saturday, 4 April 2020

3 Blank paper
1 waits
4 too long for thoughts.
180

Friday, 3 April 2020

3 Thoughts crack through
1 night
4 to a still clock.
179

3 Clogged channels
1 stuck
4 with nervous silt.
178

3 Song to sleep
1 and
4 poem to wake
1 to.
177

3 Once in a
1 while
4 a long moment.
176

3 Lump on head
1 from
4 hole in stomach.
175

3 Universe
1 of
4 no mind but ours.
174

3 Higher than
1 birds
4 stars glide at night.
173

3 Sleeps or hides
1 some
4 thing internal.
172

3 Pieces move by
1 rules
4 not yet written.
171

3 Clouds visit
1 then
4 as fog they stay.
170

3 Distant duck
1 bobs
4 like something else.
169

3 Not above
1 the
4 belows but in
1 them.
168

3 Yesterday
1 comes
4 by starlight to
1 day.
167

3 It's always
1 not
4 now somewhere else.
166

Thursday, 2 April 2020

3 Keys jingle
1 a
4 nervous ditty.
165

3 Night shadows
1 sneak
4 past eyes closed tight.
164

3 Angled paths
1 from
4 now to muich later.
163

3 One word said
1 in
4 seconds can take
1 years
5 to hear and unhear.
162

3 Para to
1 your
4 sympathetic.
161
It's all about nerves.

3 Today is
1 the
4 largest number.
160
Sometimes to infinity and beyond isn't a journey worth taking.

3 One bottle
1 two
4 glasses no words.
159
Ideally.

3 Habit fades
1 new
4 growth into old
1 soil.
158

Wednesday, 1 April 2020

3 Time of death
1 some
4 time during life.
157

3 Ends motion
1 slow
4 fall back from here.
156

3 Love is a
1 word
4 and words are love-
1 ly.
155

3 Burdens of
1 math
4 of subtraction.
154

3 Passport stamps
1 fade
4 evaporate.
153

3 Coin with hole
1 are
4 you all my change?
152

3 Counting tears
1 with
4 economics.
151

3 City life
1 late
4 night city death.
150

3 When an eye
1 feels
4 it seels colour.
149

3 Around bend
1 find
4 straight lines of light.
148

3 Pass through all
1 things
4 whispering no
1 thing.
147

3 Between beats
1 lush
4 echo valleys.
146

3 Tiny gap
1 then
4 electric touch.
145

3 Slippery
1 time
4 grab it to lose
1 it.
144

3 Words on page
1 are
4 the chatter of
1 nerves.
143

3 For all we
1 know
4 there are things we
1 don't.
142

Tuesday, 31 March 2020

3 Panic can
1 wait
4 for tomorrow.
141

3 Regrets live
1 on
4 curves not tangents.
140
Every conversation carries a small poetic chance.

3 Small chances
1 are
4 never zero.
139

3 Month's last day
1 waits
4 for another
1 year.
138

Monday, 30 March 2020

3 Problems greet
1 us
4 in the morning.
137

3 Small voices
1 now
4 clear in silence.
136

3 Sound of trees
1 you
4 have always been
1 there.
135
Inspired by Edna St. Vincent Millay's City Trees

3 Directions
1 are
4 all of forward
1 kind.
134

Saturday, 28 March 2020

3 Sadness need
1 not
4 be sad just deep.
133

3 Future filled
1 with
4 minutes from past.
132

3 Let's just go
1 and
4 buy some paper.
131

3 I'm not one
1 to
4 say I can't be
1 two.
130

3 Molecules
1 in
4 action against
1 me.
129
Consider that kinetics were never in your favour.

3 Nearness shows
1 its
4 extreme distance.
128
You cannot have hot without cold. You cannot have together without apart.

3 It's hard but
1 not
4 complicated.
127
Most problems are solved with effort and not necessarily clever thinking.

3 Plenty of
1 room
4 yet on the curve.
126
I despise long tails.

3 Travel some
1 where
4 inside of you.
125
Plenty of room at the bottom (R. Feynman).

3 Everything
1 is
4 too brief or too
1 long.
124
Life has no Goldilocks zone.

3 We have all
1 the
4 time in an out
1 break.
123

3 It was all
1 ways
4 the other twin.
122

Friday, 27 March 2020

3 Hello world
1 are
4 you worth greeting?
121

3 All curves are
1 meant
4 to be ahead
1 of.
120

3 Problem solve.
1 If
4 angry trouble
1 shoot.
119

3 Soon slips in
1 to
4 later never.
118

Thursday, 26 March 2020

3 Dull ache in
1 side
4 by side close friend.
117

3 No sense of
1 a
4 present or even
1 past.
116

3 Universe
1 of
4 indifferent
1 parts.
115

3 Exceptions
1 are
4 sometimes the rule.
114

3 Coffee old
1 friend
4 with intimate
1 warmth.
113
I hug my cup everyday.

Wednesday, 25 March 2020

3 Non-answers
1 are
4 questions disguised.
112

3 Base pair change
1 not
4 in your favour.
111
Genomes sometimes change their minds. For the worse.

3 Two birds on
1 rock
4 together a
1 part.
110

3 No thanks no
1 luck
4 keeps fates sleeping.
109
Chance does not accomodate consistently. The fates are Clotho (the Spinner), Lachesis (the Alloter) and Atropos (the Inflexible).

3 Why is how
1 when
4 who becomes what.
108

3 Not all change
1 is
4 evolution.
107

Tuesday, 24 March 2020

3 Equation
1 for
4 diffusion of
1 tears
5 is not closed in form.
106
An equation is a closed-form solution if it solves a given problem in terms of functions and mathematical operations from a given generally-accepted set (Wolfram MathWorld)

3 Absolute
1 null
4 temperature
1 is
5 also a feeling.
105

3 Gods act in
1 plays
4 put on by us.
104

3 High to low
1 and
4 one sigh between.
103

3 Sinking in
1 far
4 beyond bottom.
102

3 Bad timing
1 con-
4 verge in breaking.
101

3 The fix is
1 in
4 not the fixing.
100
Once written the piku has its own vitality and should not be altered.

3 Foreign words
1 make
4 new bumps on brain.
99
One of the translations of "bossa nova" is "new bump". Story goes that once you learn something, your brain develops a new ridge or bump (gyrus) where this knowledge is stored. Dancing bossa or learning languages gives you a new bump!

3 Strike once strike
1 hard,
4 then soft decay.
98

3 The choice isn't
1 mine.
4 I miss when it
1 was.
97
If ever.

3 Too small to
1 see,
4 too big to cope.
96
Invisible enemies get +1 for stealth and rolls 2d20 initative.

3 Paper be
1 comes
4 an ear for words.
95

3 People with
1 out
4 symptomps: you're next.
94
"People Without Symptoms" is a great band name for these COVID-19 times.

3 Let me be
1 clear:
4 future opaque.
93

3 Dignified
1 greed:
4 toilet paper.
92
Don't be a covidiot.

3 Battery
1 dead
4 or pause on self?
91

3 Triage, see
1 the
4 signs of the times.
90

3 Art and dark
1 mix
4 and you're the light.
89

3 Flatten this.
1 God
4 damn it all twice.
88

3 Words warm wrap
1 for
4 isolation.
87

3 Olympics
1 dream:
4 citius, altius,
1 dead.
86
The Tokyo 2020 Olympics are postponed to 2021. But they'll still be called the 2020 olympics. Likely because there's a mascot song that rhymes with 2020.

3 Can't find the
1 stop
4 button. Stuck on
1 play.
85

Monday, 23 March 2020

3 News cycle
1 with
4 no working brakes.
84

3 Movement with
1 full
4 paralysis.
83

3 Dry firm land
1 makes
4 this sea sickness.
82

3 Hint of worlds
1 in
4 pins of sky light.
81

3 Practised by
1 stars:
4 stellar distance.
80

Sunday, 22 March 2020

3 Store shelves too
1 have
4 their own colour.
79

3 Virus, you
1 done
4 with copier?
78

3 Mind full gone
1 are
4 nooks for questions.
77

3 Late mornings
1 roll
4 into early
1 nights.
76

3 A strange day
1 strange
4 actions invites.
75

3 Not first or
1 last
4 in between feels
1 good.
74

3 Hello spring
1 you're
4 a trap this time.
73

3 Stores empty
1 as
4 hospitals full.
72

3 We're numbers:
1 ones
4 but not zeros.
71

3 Life, a stat
1 test
4 with an n of
1 1.
70

Saturday, 21 March 2020

3 Anytime
1 each
4 time all the time.
69

3 Lips part, out
1 fly
4 tiny quiets.
68

3 Left or right?
1 Ok,
4 let's go with or.
67

3 Here's the thing:
1 it's
4 a lot of things.
66

3 Grow blind to
1 things
4 not worth seeing.
65

3 Eye caught by
1 line
4 to I don't know.
64

3 One minute
1 kiss
4 fills and hour.
63

3 Clock's right hand,
1 what
4 are you ticking
1 now?
62

3 Value in
1 not
4 assigning it.
61

3 Book of life,
1 her
4 horror story.
60

3 Microscape
1 sad
4 tiny valleys
1 dim.
59

3 Boulders roll
1 over
4 pretty flowers.
58

3 Post mortem:
1 an
4 after your thought.
57

3 Pre mortem
1 does
4 up the ante.
56

Friday, 20 March 2020

3 Regular
1 words
4 with curious use.
55

3 Large numbers
1 hide
4 me you and us.
54

3 Roads end where
1 fields
4 sway flowers bloom.
53

3 You are me
1 as
4 I see you to
1 day.
52

3 Before act
1 post
4 thought buzz of nerve.
51

3 Receipt in
1 valid.
4 Stuck with this shit.
50

3 Faith hope vision:
1 same
4 but with different
1 god.
49

3 Who are we
1 to
4 say we are some
1 one?
48

3 Eyes on ends
1 can
4 not see new starts.
47

3 Sweet melon
1 bread
4 warm dough bubble.
46

3 Words that say
1 no
4 thing sink like stones.
45

3 Important
1 things
4 hide and seek for-
1 ever.
44

3 Winter has
1 come.
4 Why in the spring?
43

3 New is the
1 new
4 new. Miss the old.
42

Thursday, 19 March 2020

3 All hands on
1 deck.
4 All feet below.
41

3 Oh virus,
1 thy
4 spring's play I see
1 through.
40

3 History
1 now
4 to yesterday.
39

3 New piku
1 age
4 fast like the times.
38

3 Outbreak unites
1 big
4 with the very small.
37

3 Bird song chirp
1 sound
4 that is always
1 there.
36

3 I prefer
1 calm
4 after the storm.
35

3 Isolate:
1 the
4 new fight or flight.
34

3 Windows doors
1 closed
4 opened new tab.
33

3 Tick tock tick,
1 tock.
4 News start and stop.
32

Wednesday, 18 March 2020

3 Further than
1 feel,
4 closer than see.
31

3 Virus, bro,
1 what's
4 with the anger?
30

3 Questions burn
1 but
4 answers pending.
29

3 Everything
1 mixed
4 in bad order.
28

3 Pixels glow
1 bits
4 a stranger now
1 friend.
27

3 Maybe runs
1 fast
4 to yes. Please, no.
26

3 Spring comes out
1 to
4 an empty stage.
25

3 The whole world
1 knocks
4 to be let out.
24

3 By strange times
1 touch
4 a stranger's face.
23

3 Unseen words
1 slip
4 past unseeing
1 eyes.
22

Tuesday, 17 March 2020

3 Just in time
1 right
4 now is too late.
21

3 Yesterday's
1 wrong
4 step brings me here.
20

3 Sunlight even
1 through
4 darkest hour.
19

3 Straight most times
1 beats
4 exponential.
18

3 Past midnight
1 comes
4 a slow new day.
17

Monday, 16 March 2020

3 People far
1 apart
4 hearts close in part.
16

3 Questions, locked
1 doors.
4 Where are the keys?
15

3 Sound of crows.
1 Omen,
4 or just birds talking.
14

3 There is no
1 after-
4 life but there is
1 after
5 life a different life.
13

3 Nerves tickle
1 but
4 without giggling.
12

3 What is left
1 grows
4 into tomorrow.
11

3 Dance and sing
1 life
4 plays the music.
10

Sunday, 15 March 2020

3 Memories
1 light
4 dust in the mind.
9

3 Thought on thought
1 stacks
4 like sediment.
8

3 Words chase words
1 then
4 period like this
1 one.
7

3 Ducks on pond
1 paired
4 except this one.
6

3 Unknown ends
1 un-
4 known beginnings
1 start.
5

Saturday, 14 March 2020

3 Contact lost
1 alone
4 blurry faces
1 far
5 on the horizon.
4

3 Understand
1 more,
4 fear less. Marie was
1 right.
3

3 Reason on
1 brain
4 kindness in heart.
2

3 Pi never
1 ends
4 unlike outbreaks
1

VIEW ALL

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.

Blank paper
waits
too long for thoughts.

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)