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20th: let's do it again


See you at Shonan Meeting 167 — Formalizing Biomedical Visualization


data visualization + celebration

Genome Sciences Center 20th Anniversary Clothing, Music, Drinks and Art

On 15 November 2019, the Genome Sciences Center held its 20th anniversary celebration.

Here you can read about the design of the evening's clothing, music, drinks and other art.

Distrust any enterprise that requires new clothes.
— Henry David Thoreau (Walden)

clothing

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Luke and Mayia wearing limited edition volunteer t-shirts. The pattern reproduces the human genome with chromosomes as spirals. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Dr. Mungall revealing his personal side: DNA socks. In his hand, the 'improved outcome', one of the signature cocktails created for the celebration. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Paul and Nazanin show off their party swag. (zoom)

t-shirt

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The relative lengths of human chromosomes. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Human chromosomes proportionately represented as spirals. Maybe you can notice something about the start and direction of each spiral. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Chromosome spirals snuggled into a square. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Chromosome spiral t-shirt design. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Knitted tag signalling the authenticity of the anniversary swag. (zoom)

socks

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Left- and right-handed forms of DNA. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Dimensions of the DNA molecule. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Sock design. The left sock DNA is left-handed and the right sock DNA is right-handed. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The knitted socks, as they should be worn. The dots at the small toe indicate the left and right socks. (zoom)

hoodie

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Warm and cozy hoodie has the GSC logo unwound on the left arm. The anniversary patch is on the back right. (zoom)

lanyard

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The lanyard shows two DNA helices zipping up.
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news + thoughts

Using Circos in Galaxy Australia Workshop

Thu 20-02-2020

A workshop in using the Circos Galaxy wrapper by Rasche and Hiltemann. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Using Circos in Galaxy Australia workshop. (zoom)

Download workshop slides.

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).

Essence of Data Visualization in Bioinformatics Webinar

Thu 20-02-2020

My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Essence of Data Visualization in Bioinformatics webinar. (zoom)

Download webinar slides.

Markov models — training and evaluation of hidden Markov models

Thu 20-02-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Markov models — training and evaluation of hidden Markov models. (read)

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

Tue 28-01-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Luke and Mayia wearing limited edition volunteer t-shirts. The pattern reproduces the human genome with chromosomes as spirals. (zoom)

As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Precisely engineered frame mounts of flow cells used to sequence genomes in our laboratory. (zoom)

Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The plaque at the back of one of the framed Illumina flow cell. This one has sequence from a patient's lymph node diagnosed with Burkitt's lymphoma. (zoom)

Scientific data visualization: Aesthetic for diagrammatic clarity

Mon 13-01-2020

The scientific process works because all its output is empirically constrained.

My chapter from The Aesthetics of Scientific Data Representation, More than Pretty Pictures, in which I discuss the principles of data visualization and connect them to the concept of "quality" introduced by Robert Pirsig in Zen and the Art of Motorcycle Maintenance.

Yearning for the Infinite — Aleph 2

Mon 18-11-2019

Discover Cantor's transfinite numbers through my music video for the Aleph 2 track of Max Cooper's Yearning for the Infinite (album page, event page).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Yearning for the Infinite, Max Cooper at the Barbican Hall, London. Track Aleph 2. Video by Martin Krzywinski. Photo by Michal Augustini. (more)

I discuss the math behind the video and the system I built to create the video.