resources
visualizations
presentations
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`
Numbers are a lot of fun. They can start conversations—the interesting number paradox is a party favourite: every number must be interesting because the first number that wasn't would be very interesting! Of course, in the wrong company they can just as easily end conversations.
did you see something special?
These three numbers have the curious property that they are almost Pythagorean. In other words, if they are made into sides of a triangle, the triangle is nearly a right-angled triangle (89.1°).
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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.
Patience but know where to put it.
Favourite looks words tastes phrases ex foreign origins.
Melody same feelings different.
Desire life remote control.
Sun rays burn off night dust into day.
Sanitize in perfection now.
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.
