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lunch break
Distractions and amusements, with a sandwich and coffee.
visualization + design
They serve as the form for The Outbreak Poems.
The art of Pi (`\pi`), Phi (`\phi`) and `e`
Like music with numbers? Here's a short list of some of my favourite songs that have numbers in their lyrics. Absolutely none of them is about bottles of beer.
music with numbers
1 — One Hundred Billion Sparks, Max Cooper | Imagine a neuron firing. Now imagine 100,000,000,000 neurons firing. This is the music for it.
2 — Numbers, Smoke City | This song is entirely composed of references to different numbers. The bonus? It's both in English and Portuguese. I love the way it ends—"Isn't it beautiful out here?".
Un
Un
Four
Five
Fifteen
Quinze
Seventeen
Seven
...
Tres
forty nine
Isn't it beautiful out here?
Isn't it beautiful out here?
Isn't it beautiful out here?
3 — 99 luftbaloons, Nena | The numerical classic.
Hast du etwas Zeit für mich
Dann singe ich ein Lied für dich
Von 99 Luftballons
4 — One, Aimee Mann | Beautiful mathematics of relationships using small numbers.
One is the lonliest number that you'll ever do. Two can be as bad as one, it's the lonliest number since the number one.
5 — Angels at My Door, Una | Long sequences of numbers.
58, 56, 54 angels at my door.
63, 62, 61, 60, 59, 58 angels at my gate.
6 — Tricky, Tricky, Royksopp | Number words about the fearful six from Norway.
Six afraid of seven 'cause seven, eight, nine
I'm about to lose it the second time
7 — Pt vs Ys, Yoshinori Sunahara | The first four numbers, in German, are this song's lyrics.
Eins, zwei, drei, vier.
8 — Der Kommissar, Falco | Unlike the previous song, this one starts with a German count (doesn't get to vier, though) and just gets better from there.
Two, three, four
Eins, zwei, drei
Na, es is nix dabei
Na, wenn ich euch erzähl' die G'schicht'
9 — 2wicky, Hooverphonic | The numbers likely reference the Prophet-600 and SH-101 synthesizers.
Prophet 60091.
Before we start you should know that you're not the only one who can hurt me.
SH10151.
This is the serial number of our orbital gun.
SH10151.
You better be sure before you leave me for another one.
10 — Straight to Number One, Touch and Go | Something to listen to after midnight.
Fingers, four, play, three, to number one.
11 — The Beat Experience, Pepe Deluxe | I am reminded of this song at too many academic seminars.
Here we are now, at the middle, of the fourth large part of this talk.
More and more I have the feeling that we are getting nowhere.
Slowly, as the talk goes on, we are getting nowhere.
And that is a pleasure.
It is not irritating where one is.
It is only irritating to think one would like to be somewhere else.
Here we are now, a little bit after the middle, of the fourth large part of this talk.
12 — Thousand Kisses Deep, Leonard Cohen | A list of songs that doesn't include one by Cohen is not worth reading. The sentiment of a thousand kisses is as old as lips existed. Catullus wrote to Lesbia "da mi basia mille, deinde centum, dein mille altera, dein secunda centum, deinde usque altera mille, deinde centum" [Give me a thousand kisses, then a hundred, then another thousand, then a second hundred, then yet another thousand, then a hundred.] Well, you get the idea.
And sometimes when the night is slow,
The wretched and the meek,
We gather up our hearts and go,
A Thousand Kisses Deep.
13 — Six Seven Times, Flunk | Curiously the product here is 42. This song is the answer to life.
You've got it all
Six seven times
You've got it all
Makes me feel so fine
And it's all there is
14 — 7 seconds, Youssou N'Dour | Dreamy references to a short period of time.
7 seconds away. Just as long as I stay. I'll be waiting.
15 — 100 Billion Stars, Lux | Something to relax to while you ponder insignificance.
16 — First Picture, Nikolaj Grandjean | First is the most memorable number.
I remember
The first picture
One million different shadows
Where we've been around the willows
17 — Millions of Millions, Music for a French Elevator | Very desirable. And I can't believe I transcribed the whole thing.
5.50 million dollars, 2.6775 and very desirable 8 million dollars 5.6 million and 2.4 million 3.4 million and 2.9 million 1.2 would've amounted to 4 million 1.2 million 19.4 million 6.6 million 5.275 million 1.2 million 3-and-a-half million dollars 6.453 million 8 million 5.050 million 1.4 million close to a million dollars 933.5 million 3.8 million 5 million dollars 2-and-a-half million 600 million dollars can you shut the door? 3-and-a-half million dollars 2.5 million .050 million 572,750 thousand 5.050 million 3.8 million 3 million 150 thousand 8 million 419.5 million
18 — Love Potion #9, The Searchers | I started kissing everythying in sight.
It smelled like turpentine, it looked like Indian ink
I held my nose, I closed my eyes, I took a drink.
19 — 93 Million Miles, Luan Santana feat. John Kip | A little sticky, a little sweet but it makes up for the fact that much of it is in Portuguese.
But the absence of the light is a necessary part.
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news + thoughts
Virus Mutations Reveal How COVID-19 Really Spread
Genetic sequences of the coronavirus tell story of when the virus arrived in each country and where it came from.
Our graphic in Scientific American's Graphic Science section in the June 2020 issue shows a phylogenetic tree based on a snapshot of the data model from Nextstrain as of 31 March 2020.
Cover of Nature Cancer April 2020
Our design on the cover of Nature Cancer's April 2020 issue shows mutation spectra of patients from the POG570 cohort of 570 individuals with advanced metastatic cancer.
The cover design accompanies our report in the issue Pleasance, E., Titmuss, E., Williamson, L. et al. (2020) Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer 1:452–468.
Modeling infectious epidemics
Every day sadder and sadder news of its increase. In the City died this week 7496; and of them, 6102 of the plague. But it is feared that the true number of the dead this week is near 10,000 ....
—Samuel Pepys, 1665
This month, we begin a series of columns on epidemiological models. We start with the basic SIR model, which models the spread of an infection between three groups in a population: susceptible, infected and recovered.
We discuss conditions under which an outbreak occurs, estimates of spread characteristics and the effects that mitigation can play on disease trajectories. We show the trends that arise when "flattenting the curve" by decreasing `R_0`.
This column has an interactive supplemental component that allows you to explore how the model curves change with parameters such as infectious period, basic reproduction number and vaccination level.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.
The Outbreak Poems
I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.
That moment when you know a moment.
Branch to branch, flit, look everywhere, chirp.
Memory, scent of thought fleeting.
Distant pasts all ways in plural form.
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses
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.
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.
Using Circos in Galaxy Australia Workshop
A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.
Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).