Without an after or a when.can you hear the rain?more quotes

# computing: numerical

2020 $\pi$ day art and the piku

# data visualization + art

Like algorithms?
Enjoy even more $\\pi$ art.

# Hola Mundo and Hello $\pi$

Art is science in love.
— E.F. Weisslitz

Remix of the cover design of Hola Mundo by Hannah Fry. (zoom)
Remix of the cover design of Hola Mundo by Hannah Fry. (zoom)
Remix of the cover design of Hola Mundo by Hannah Fry. (zoom)

## art and algorithms

Some algorithms connect us and some keep us apart—we need them to remind us what it is to be human and what it is to be a computer.

My cover design for Hannah Fry's Hello World: Being Human in the Age of Algorithms is based on my 2013 $\pi$ Day art. The book is published by Blackie Books.

Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Published by Blackie Books. Cover design by Martin Krzywinski. The front cover of the book shows a network based on the first 1,418 digits of $\pi$. (zoom)
Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Published by Blackie Books. Cover design by Martin Krzywinski. The back cover of the book shows a network based on the first 837 digits of $\pi$. (zoom)

## creating the cover

The cover begins with a 57 × 35 matrix of 1,995 colored circles. Each circle encodes a digit of $\pi$, starting with 3.1415.... Inside each circle is a smaller circle whose color is based on the next digit. The radius of the inner circle is $1/\phi^2$ where $1/\phi = 0.618$ is the Golden Ratio.

The beginning of the cover design. 1,995 colored circles encode digits of $\pi$. (zoom)
Each circle has a smaller circle inside it that encodes the next digit. (zoom)

Once the circles are drawn, neighbouring circles that correspond to the same digit are connected with thick lines. The thickness of these lines is $t_0 = 3/(2\phi^2)$, relative to the outer circle radius. Circles that correspond to digits whose difference is $1$ or $-1$ are connected by a slightly thinner line with thickness $t_1 = t_0/\phi$.

Neighbouring identical digits are connected with thick lines. (zoom)
Neighbouring digits that are off by 1 are connected by thinner lines. (zoom)

More lines are drawn that connect digits with a larger difference, $|d| > 1$. The thickness for these lines is $t_d = t_0/\phi^{|d|}$. When all differences up to $|d| < 6$ are accounted for, we get a pleasant jumble of lines.

Neighbouring digits whose difference is greater than one are connected by progressively thinner lines. (zoom)
Circles representing the digits of $\pi$ with all lines connecting neighbouring digits. (zoom)

To accommodate the title and other text on the cover, the design was generated by avoiding drawing any circles within a certain distance of the text.

This way, the network of digits wraps around the text. In the final design, the front page has 1,418 digits and the back has 878 digits.

Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Cover design by Martin Krzywinski. (zoom)
Hola Mundo by Hannah Fry. Translation by Francisco J. Ramos Mena. Cover design by Martin Krzywinski. (zoom)

## cover remixes

### just the lines

Just the connecting lines. (zoom)
Triangle color is the average color of their corners. (zoom)
Inner circles punched out. (zoom)
Just the triangles. (zoom)

# 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.

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

# 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.

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.

Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
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.

Using Circos in Galaxy Australia workshop. (zoom)

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.

Essence of Data Visualization in Bioinformatics webinar. (zoom)

# 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.

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.

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.

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.

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.

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)