resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
visualization + design
They serve as the form for The Outbreak Poems.
`pi` Day 2013 Art Posters
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. I sympathize with this position and have `\tau` day art too!
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.
2013 was the first year in which I made `\pi` day art. It was a year of dots and love.
René Hansen has created an interactive version of this year's posters! Why not go to the Feynman point directly!
shimmering dots
The posters explore the relationship between adjacent digits in `\pi`, which are encoded by color using the scheme shown above. The design appears to shimmer due to the luminance effect. In some versions of the poster, adjacent identical (or similar) digits are connected by lines.
The recipe for each poster is included in its figure legend. It gives the color of the `i`th outer and inner circles. `\pi_i` is used to represent the `i`th digit of `\pi`. For example, the recipe
`\pi_i` / `\pi_{i+1}`
corresponds to the case where outer circle color encodes the `i`th digit and the inner circle color encodes the next digit `i+1`th. In this scheme, inner and outer circles of adjacent positions have the same color.
The posters were generated automatically with a Perl script that generated SVG files. Post processing and layout was done in Illustrator. If you are interested in depicting your favourite number this way, let me know.
The design was inspired by the beautiful AIDS posters by Elena Miska.
love in `\pi`—you can find it here
I calculated `pi` to 13,099,586 digits and then I found love.
It's fun to look for digits or look for words in `\pi`.
Just don't get carried away. Because `\pi` is likely normal in base 10, all words and all patterns appear in it, somewhere.
I wanted to know the first time that "love" appears in `\pi`. When encoded using the scheme a=0, b=1, ..., z=25, "love" is the digit sequence 1114214.
This sequence appears first at position 13,099,586 (...892199163111142148187311392...). And, of course, infinitely many times after that.
Curiously, "hate" (0700194) appears well before love, at digit 514,717. In the first 200,000,000 digit "hate" appears 23 times, 6 times more than "love".
If you use the scheme a=1, b=2, ..., z=26, then "love" becomes 1215225. This is first seen at 6,317,696 (...610311912912152256606850141...).
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news + thoughts
The Outbreak Poems
I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.
Door closes next next door closes next nothing is left open.
One of the pair is from the other.
Eyes look at eyes and see themselves.
Look back and pass destinations.
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).
Essence of Data Visualization in Bioinformatics Webinar
My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.
Markov models — training and evaluation of hidden Markov models
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.
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
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.
As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.
Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.
