resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
data visualization + art
especially a short one.
Infinity in Just Over Six Minutes
To see a World in a grain of sand,
And Heaven in a wild flower,
Hold Infinity in the palm of your hand
And Eternity in an hour.
— William Blake
In collaboration with Max Cooper, we told a story about infinity in 6 minutes and 34 seconds.
This was the Aleph 2 track on Max's latest album, Yearning for the Infinite.
In science one tries to tell people,
in such a way as to be understood by everyone,
something that no one ever knew before.
But in poetry, it’s the exact opposite.
—Paul Dirac, Mathematical Circles Adieu by H. Eves [quoted]
We chose a low-fi terminal style using the Classic Console font by Csaba Széll. I extended the font to include more set theory symbols.
The animation was closely synchronized to the music, all the while trying to avoid looking too much like something from the Matrix movie.
These pages describe the system I build to generate the animation and the mathematics behind infinity, including sets, cardinality, countability, $\aleph$ and the Continuum Hypothesis.
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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.
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
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.
