Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
Tango is a sad thought that is danced.Enrique Santos Discépolothink & dancemore quotes

pi: exciting


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


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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 2017 Art Posters - Star charts and extinct animals and plants


Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2017 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` approximation day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2015 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` approx day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2013 `\pi` day

Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
All art posters are available for purchase.
I take custom requests.

Caelum non animum mutant qui trans mare currunt.
—Horace

This year: creatures that don't exist, but once did, in the skies.

And a poem Of Black Body.

This year's `\pi` day song is Exploration by Karminsky Experience Inc. Why? Because "you never know what you'll find on an exploration".

If you like space, you'll love my the 12,000 billion light-year map of clusters, superclusters and voids. Find the biggest nothings in Boötes and Eridanus.

create myths and contribute!

Want to contribute to the mythology behind the constellations in the `\pi` in the sky? Many already have a story, but others still need one. Please submit your stories!

Here I make available all the files you need to reconstruct the chart. All files are plain text and designed to be easily parsable.


Pi Day 2017 Art Posters - Star charts and extinct animals and plants
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Star chart of the first 12,000,000 digits of `\pi`. The 80 constellations honor extinct animals and plants. Azimuthal equidistant projection. (BUY ARTWORK)

For the simplest chart, you'll need the star catalogue which already provides the longitude and latitude coordinates for each star. It'll be up to you to choose and calculate a projection.

You can then layer constellations, which are defined by a list of edges. If you like, you can draw boundaries around each constellation, which are also provided.

Star-to-constellation mapping is also given, which allows you to create labels for the stars within each constellation based on relative brightness.

Finally, you can get the species details for each constellation, including the Latin name of the species, Wikipedia URL and (for many) the mythology of the constellation.

star catalogue

The star catalog generated from the first 12 million digits of `\pi`.

DOWNLOAD

#   idx       digits   name      x      y      z     long      lat      dist  mabs  mapp
      0 314159265358      a  -1859    926     35  145.339   38.384  2077.157  3.00 14.59
      1 979323846264      b   4793  -2616    126  -38.404  -39.555  5461.884 -1.00 12.69
      2 338327950288      c  -1617  -2205   -472 -110.162   32.164  2774.797  3.00 15.22
      3 419716939937      d   -803  -3307    493 -105.489    3.655  3438.620  2.00 14.68
...
 999996 601538500580  cexhk   1015  -1150   -442  -48.144  -14.704  1596.273 -5.00  6.02
 999997 420478142596  cexhl   -796   2814   -241   97.939   14.471  2934.330  1.00 13.34
 999998 278256213419  cexhm  -2218    621   -159  156.900   46.719  2308.776  4.00 15.82
 999999 453839371943  cexhn   -462  -1063   -306  -95.924   26.937  1198.770 -2.00  8.39

constellation definitions

Constellations were manually defined. Each constellation has a name and abbreviation (first 3 characters unless longer is required to uniquely specify it). Shown next is the number of stars used to define the constellation and their names, as appear in the star catalogue file above. Next is the number of edges and the star pairs that define the edges of the constellation. The edges are not in any particular order and have no direction. Any spaces in names are encoded with _.

DOWNLOAD

# idx n_stars n_edges name abbrev stars edges
 ...
 2  3  3                   alaotra     ala blts,btosf,cbkbw btosf-cbkbw,blts-btosf,blts-cbkbw
 3  4  4                 alloperla     all ghyr,pwkn,ssrx,ugwt pwkn-ssrx,pwkn-ghyr,ugwt-pwkn,ssrx-ghyr
 4  2  1                   aplonis     apl cbocd,rllm rllm-cbocd
 ...

You can use this file to quickly search for certain shapes. For example, triangular constellations are those that have 3 stars and 3 edges.

> grep " 3  3" constellations.def.txt
 2  3  3                   alaotra     ala blts,btosf,cbkbw btosf-cbkbw,blts-btosf,blts-cbkbw
16  3  3                   camptor    camp benxf,bqvh,bwqed bqvh-benxf,bwqed-bqvh,bwqed-benxf
26  3  3                  desmodus     des bfnqu,mork,zwzy bfnqu-mork,zwzy-bfnqu,zwzy-mork
27  3  3                ectopistes     ect bopmt,cbquf,wmnw cbquf-bopmt,wmnw-cbquf,wmnw-bopmt
30  3  3                    hoopoe     hoo bpsop,bvmjh,tryh tryh-bvmjh,bpsop-tryh,bpsop-bvmjh
31  3  3                      huia     hui ccteo,xbvq,yqet xbvq-yqet,ccteo-xbvq,ccteo-yqet
39  3  3               malpaisomys     mal bucqd,likq,nqn nqn-bucqd,likq-nqn,likq-bucqd
41  3  3                   mariana     mar gmps,jydb,pcjx pcjx-gmps,jydb-pcjx,jydb-gmps
49  3  3          palaeoaldrovanda     pal bedae,oife,saz bedae-saz,oife-bedae,oife-saz
63  3  3                    rhynia     rhy bpviv,cenuk,hivz bpviv-hivz,cenuk-bpviv,cenuk-hivz
65  3  3                  silphium     sil bjesg,bmquw,bpxia bmquw-bpxia,bjesg-bmquw,bjesg-bpxia
69  3  3                   tadorna     tad bukqe,cbtrx,epdx cbtrx-epdx,bukqe-cbtrx,bukqe-epdx
72  3  3                 traversia     tra fcnw,fywb,puib fywb-fcnw,puib-fywb,puib-fcnw
80  3  3                  yersinia     yer colq,ibls,zgvy ibls-zgvy,colq-ibls,colq-zgvy

constellation boundaries

The boundaries were manually defined. Shown here, for each constellation, is the constellation's area, perimeter center and boundary `(x,y)` pairs, delimited by : and represent a closed polygon that encloses the constellation's stars.

All values are longitude and latitude. The three constellations listed below are ones with smallest area.

DOWNLOAD

# abbrev area perimeter centroid_xy boundary_xy_pairs

...
com 74.83 34.96 -102.50,26.25 -100.00,30.00:-102.50,30.00:-105.00,30.00:-107.50,30.00:-107.50,27.50:
			      -107.50,25.00:-107.50,22.51:-105.00,22.51:-102.50,22.51:-100.00,22.51:
			      -97.51,22.51:-97.51,25.00:-97.51,27.50:-97.51,30.00:-100.00,30.00
pal 50.02 30.00 3.43,-40.93 5.00,-37.49:2.50,-37.49:0.00,-37.49:0.00,-40.00:0.00,-42.50:0.00,-45.00:
			    2.50,-45.00:5.00,-45.00:5.00,-42.50:7.49,-42.50:7.49,-40.00:7.49,-37.49:5.00,-37.49
sil 37.57 25.02 115.00,-51.25 115.00,-47.50:112.49,-47.50:112.49,-50.00:112.49,-52.49:112.49,-55.00:
    	  		      115.00,-55.00:117.50,-55.00:117.50,-52.49:117.50,-50.00:117.50,-47.50:115.00,-47.50

The boundary polygons abut but do not overlap and they cover the entire sky. There is one polygon per consetllation. The total area of all constellations is `360 × 180 = 36800`.

constellation star membership

This is a list of all the stars on the chart and their constellation membership. A star is considered to be in a constellation if it falls within the constellation boundary.

The `i` and `j` indexes give the relative brightness of the star on the map and in the constellation, respectively. If a star is used to define the constellation edges it gets a + otherwise -.

DOWNLOAD

# abbreviation star i j mapp on_edge?
     aep bkawv     35     0   1.34 +
     aep   gql     65     1   1.63 +
     aep cavix     72     2   1.71 +
     aep bqxvm    137     3   2.25 +
     aep  tjow    158     4   2.31 +
     aep beelq    176     5   2.39 +
...
     yer  jjlj  39365   412   7.24 -
     yer bgswm  39464   413   7.24 -
     yer  ittu  39546   414   7.24 -
     yer  wakp  39556   415   7.24 -
     yer bedks  39667   416   7.25 -
     yer  gxzo  39817   417   7.25 -

To lookup the 10 brightest stars, sort on the i index. Here we see that megal (Megalodon) has the brightest star in the sky, jkxo with apparent magnitude `-2.05`. The next two brighest stars are in mam (Mammuthus) and ara (Araucaria).

> cat constellations.stars.txt | sort -n +2 -3 | head -10
   megal  jkxo      0     0  -2.05 +
     mam btsqy      1     0  -0.73 +
     ara ccijs      2     0  -0.38 +
     rap btaum      3     0   0.26 +
     urs bxlss      4     0   0.26 +
     tec bgrdk      5     0   0.43 +
     cop  itwr      6     0   0.45 +
     ara  mrvq      7     1   0.54 +
     phe  loju      8     0   0.54 +
     mam bhlbw      9     1   0.55 +

To get a list of the brightest star in each constellation, just search for " 0 ". Below I show this list sorted by brightness.

> cat constellations.stars.txt | grep " 0 "| sort -n +4 -5 
   megal  jkxo      0     0  -2.05 +
     mam btsqy      1     0  -0.73 +
     ara ccijs      2     0  -0.38 +
     rap btaum      3     0   0.26 +
     urs bxlss      4     0   0.26 +
     tec bgrdk      5     0   0.43 +
     cop  itwr      6     0   0.45 +
     phe  loju      8     0   0.54 +
     kel bnhwx     11     0   0.59 +
     spe  rtep     13     0   0.71 +
     ...
     nes  vxou    299     0   2.80 -
     aur bmjvf    307     0   2.81 +
     tra  puib    318     0   2.83 +
     pip  cecq    358     0   2.91 +
     pal  oife    389     0   2.97 +
     swa   gvr    463     0   3.12 +
     hui ccteo    485     0   3.17 +
     ple bzqur    506     0   3.20 +
     com  ygrn    875     0   3.64 +
     car  yjkn    933     0   3.68 +

For example, tec (Tecopa) has bgrdk as its brightest star, which is 6th brightest in the sky with an apparent magnitude of 0.43.

The constellation whose brightest star is dimmest of all first brightest stars is car (Caracara). Its brightest star is yjkn which is 934th brightest in the sky with an apparent magnitude of 3.68.

To get the number of stars in each constellation, just add the number of times the constellation abbreviation appears. Bron has the most stars of any constellation, more than twice as many as the next one, archaeo (Archaeopteryx). Both car (Caracara) and por (Porzana) have only 7 stars each, the fewest of all constellations.

   5230 bro
   2287 archaeo
   2205 thy
   2155 kim
   1838 archaea
   1789 came
   1768 ard
...
     20 megal
     19 swa
     17 mar
     12 rhy
      8 sil
      7 por
      7 car

constellation names, stories and links

The constellations are in no particular order in this file.

DOWNLOAD

# constellation name
# hemisphere (n north, s south, b both)
# common name
# Latin name
# extinction date
# URL
# optional story

aplonis
n
mysterious bird of Ulieta
Aplonis ulietensis
1774-1850
https://en.wikipedia.org/wiki/Raiatea_starling

desmodus
n
Giant Vampire Bat
Desmodus draculae
Pleistocene or early Holocene
https://www.thoughtco.com/recently-extinct-shrews-bats-and-rodents-1092147
It is thought that each night Desmodus flies up against the dome of the sky, looking for a way to escape.

...
VIEW ALL

news + thoughts

Find and snap to colors in an image

Sat 29-12-2018

One of my color tools, the colorsnap application snaps colors in an image to a set of reference colors and reports their proportion.

Below is Times Square rendered using the colors of the MTA subway lines.


Colors used by the New York MTA subway lines.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Times Square in New York City.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Times Square in New York City rendered using colors of the MTA subway lines.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Granger rainbow snapped to subway lines colors from four cities. (zoom)

Take your medicine ... now

Wed 19-12-2018

Drugs could be more effective if taken when the genetic proteins they target are most active.

Design tip: rediscover CMYK primaries.

More of my American Scientific Graphic Science designs

Ruben et al. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine Science Translational Medicine 10 Issue 458, eaat8806.

Predicting with confidence and tolerance

Wed 07-11-2018
I abhor averages. I like the individual case. —J.D. Brandeis.

We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.

Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Predicting with confidence and tolerance. (read)

Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.

Background reading

Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.

4-day Circos course

Wed 31-10-2018

A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Composite of the kinds of images you will learn to make in this course.

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Background reading

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.