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 2017 Art Posters - Star charts and extinct animals and plants
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.
Caelum non animum mutant qui trans mare currunt.
—Horace
This year: creatures that don't exist, but once did, in the skies.
This year's `\pi` day song is Exploration by Karminsky Experience Inc. Why? Because "you never know what you'll find on an exploration".
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!
This year I wanted to something more than visuals. Space is vast, so let's fill it with words.
I asked my good friend and poet, Paolo Marcazzan, to collaborate. I described the idea for the art—a universe of stars based on `\pi` and the extinct creatures that live within it—and asked him to find the matching words.
And they could not have been more perfect.
author's note
The poem situates the dark as a place for contention and ongoing confrontation. Whether in the recesses of space or heart, the poem probes the territory of distance, absence, uncertainty and muteness. It considers the relational as default positioning of existence (earthly, universal), and that which remains unmet within that context.
Life in its dimension of cross-grained, often broken linearity is juxtaposed with a quote form Dante that references instead his vision of sidereal circularity as the benign force that moves all things in the universe. For the earthbound, the questions and concerns remain those of identity, passage, escape from transiency, and slow tempering of hope.
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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.
Panic can wait for tomorrow.
Regrets live on curves not tangents.
Small chances are never zero.
Month's last day waits for another year.
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.
