Sun is on my face ...a beautiful day without you.be apartmore quotes

# numbers: beautiful

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

# visualization + design

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 2018 Art Posters - Stitched city road maps from around the world

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.
2017 $\pi$ day
2016 $\pi$ approximation day
2016 $\pi$ day
2015 $\pi$ day
2014 $\pi$ approx day
2014 $\pi$ day
2013 $\pi$ day
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.

All art posters are available for purchase.
I take custom requests.

And if you've got to sleep a moment on the road
I will steer for you
And if you want to work the street alone
I'll disappear for you

This year's is the 30th anniversary of $\pi$ day. The theme of the art is bridging the world and making friends. So myself I again team up with my long-time friend and collaborator Jake Lever. I worled with Jake on the snowflake catalogue, where we build a world of flakes.

And so, this year we also build a world. We start with all the roads in the world and stitch them together in brand new ways. And if you walk more than 1 km in this world, you'll likely to be transported somewhere completely different.

This year's $\pi$ day song is Trance Groove: Paris. Why? Because it's worth to go to new places—real or imagined.

The input data set to the art are all the roads in the world, as obtained from Open Street Map.

Road segments between intersections are represented by polylines and ends at intersections are snapped together to coincide with a resolution of 5–10 meters.

There are 108,366,429 polylines and together they span about 39,930,000 km.

## extracting cities

We took 44 cities and sampled a square patch of 0.6 × 0.6 degrees of roads from the data set centered on the longitude and latitude coordinates below. This roughly corresponds to a square of 65 km × 65 km.

These center coordinates might be slightly different from the canonical ones associated with a city—I used Google Maps to center the coordinates on what I felt was a useful center for sampling streets. Below are these coordinates along with the number of polylines extracted.

$CITY LATITUDE LONGITUDE POLYLINES --------------- ------------ ------------- --------- amsterdam 52.38179720 4.90840330 98,965 bangkok 13.72635950 100.53609560 154,348 barcelona 41.38759720 2.17333560 86,575 beijing 39.90487690 116.39331750 49,867 berlin 52.51864170 13.40732310 64,336 buenos_aires -34.61566250 -58.50333750 267,432 cairo 30.05371250 31.23528970 108,524 copenhagen 55.67346250 12.58781160 45,025 doha 25.28233490 51.53479620 50,458 dublin 53.34316360 -6.24433520 44,109 edinburgh 55.94884870 -3.18828100 34,211 hong_kong 22.31338230 114.16994610 36,329 istanbul 41.03592820 28.98158110 190,938 jakarta -6.21858830 106.85252890 253,211 johannesburg -26.20653880 28.05113830 128,840 lisbon 38.73064000 -9.13667460 98,118 london 51.50838960 -0.08585320 169,164 los_angeles 34.04362360 -118.24505510 193,899 madrid 40.41671290 -3.70329570 112,495 marrakesh 31.63192610 -7.98895890 17,442 melbourne -37.88286720 145.11800540 140,817 mexico_city 19.39741470 -99.15827060 273,477 moscow 55.75202630 37.61531070 40,043 mumbai 19.18775070 72.97777590 65,316 nairobi -1.28718700 36.83157870 31,317 new_delhi 28.61245350 77.21369970 262,503 new_york 40.72187290 -73.92426750 199,652 nice 43.70006260 7.26974590 25,564 osaka 34.66944300 135.49965600 376,652 paris 48.85837360 2.29229260 175,028 prague 50.08022370 14.43002100 58,659 rome 41.89659480 12.49983650 81,370 san_francisco 37.77526950 -122.40966350 82,462 sao_paulo -23.57343700 -46.63341590 267,742 seoul 37.54869140 126.99479350 169,593 shanghai 31.22590500 121.47386710 50,036 st_petersburg 59.93029690 30.33955910 31,186 stockholm 59.32318770 18.07408060 48,321 sydney -33.86772020 151.20734660 76,820 tokyo 35.69220740 139.75613010 694,893 toronto 43.66328030 -79.38932030 73,173 vancouver 49.25782630 -123.19394300 34,081 vienna 48.20740250 16.37336040 53,669 warsaw 52.23101840 21.01639680 54,870$

Each city's road coordinates were then transformed using the equirectangular projection to make the distance between longitude meridians constant with latitude. This was done by $$\phi' \leftarrow \phi - \text{avg}(\phi)$$ $$\lambda' \leftarrow (\lambda - avg(\lambda)) \text{cos} (avg(\phi))$$

where $\phi$ is the latitude and $\lambda$ is the longitude. The average is taken over the patch of roads extracted for the city. For all steps below these transformed coordinates were used.

## copenhagen

Let's look at one city—Copenhagen—to get a feel for the data set.

The roads in and around Copenhagen. (zoom)

In the zoom crop below, you can see the intersections (dots) and the individual polylines that connect the intersections.

Downtown Copenhagen. (zoom)

Zooming in even more you can see the Christiansborg Slot, one of the Danish Palaces and the seat of the Danish Parliament (corresponding Google Map view).

In and around Christiansborg Slot (red dot) in downtown Copenhagen. (zoom)

## creating city strips

City strips were created by sampling patches of 0.015 × 0.015 degrees (after transformation). This corresponds roughly to 1.7 km.

For each position in the strip, patches were sampled in order of the digits of $\pi$ only if the number of polylines in the was $40d \le N < 40(d+1)-1$ where $d$ is the digit of $\pi$. Patches for $d=9$ only need to have $360 \le N$ polylines.

For example, the first patch is assigned to $d=3$ and it must have $120 \le N < 159$ polylines. The second patch is sampled so that its density is $40 \le N < 79$ because it is associated with the next digit, $d=1$.

Further selection on acceptable patches is performed so that the streets line up with the previous patch. Minor local adjustments and stitching are performed to make the join appear seamless.

Below is an example of a set of city strips for Amsterdam, Bangkok, Beijing, Berlin, Copenhagen, Edinburgh, Hong Kong, Johannesburg, Marrakesh and Melbourne.

On the road with 10 digits of $\pi$. City strips for Moscow, Mumbai, Nairobi, New Delhi, Nice, Prague, Rome, Stockholm, Vancouver and Warsaw. (BUY ARTWORK)

Below I zoom in on a portion of the city strips above to show the result of the stitching—individual street patches are outlined in blue squares.

Close-up of stitched streets in a city strip.

It's interesting to see that some patches (e.g. 4th one on the bottom strip, which is Copenhagen) don't necessarily have roads that across the patch horizontally.

## creating world patches

World patches are a two-dimension version of city strips but they use more than one city.

Patches are sampled from cities based on the order of the digits of $\pi$, as arranged on a 6 × 6 grid. For example, the first row of patches corresponds to 314159 and the second 265358. Each digit is assigned to a city from which the corresponding patch is sampled.

As for city strips, patches are selected only if they align with previous patches. This is now trickier to do in two-dimensions because we must match a selected patch with up to two other patches already placed.

Unlike for city strips, there is no selection made for street density.

Below is a world patch using the following digit-to-city assignment: 0:Amsterdam, 1:Doha, 2:Marrakesh, 3:Mumbai, 4:Nairobi, 5:Rome, 6:San Francisco, 7:Seoul, 8:Shanghai and 9:Vancouver.

On the road with 36 digits of $\pi$. A world patch using Amsterdam, Doha, Marrakesh, Mumbai, Nairobi, Rome, San Francisco, Seoul, Shanghai and Vancouver (BUY ARTWORK)

Below I zoom in on patches in the center of the image and show the cities from which the patches were sampled.

Close-up of stitched streets in a world patch.
VIEW ALL

# 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.

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.

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.

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.

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.

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.

# Molecular Case Studies Cover

Fri 06-07-2018

The theme of the April issue of Molecular Case Studies is precision oncogenomics. We have three papers in the issue based on work done in our Personalized Oncogenomics Program (POG).

The covers of Molecular Case Studies typically show microscopy images, with some shown in a more abstract fashion. There's also the occasional Circos plot.

I've previously taken a more fine-art approach to cover design, such for those of Nature, Genome Research and Trends in Genetics. I've used microscopy images to create a cover for PNAS—the one that made biology look like astrophysics—and thought that this is kind of material I'd start with for the MCS cover.

Cover design for Apr 2018 issue of Molecular Case Studies. (details)

# Happy 2018 $\tau$ Day—Art for everyone

Wed 27-06-2018
You know what day it is. (details)