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See you at Shonan Meeting 167 — Formalizing Biomedical Visualization

communication + science

Nature Methods: Points of View

Martin Krzywinski @MKrzywinski
Points of View column in Nature Methods. (Points of View)

The first Points of View column was about color coding in the July 2010 issue of Nature Methods. In its 5 year history, the column has established a significant legacy— it is one of the most frequently accessed parts of Nature Methods. The community sees the value in clear and effective visual communication and acknowledges the need for a forum in which best practices in the field are presented practically and accessibly.


Bang Wong, in collaboration with visiting authors (Noam Shoresh, Nils Gehlenborg, Cydney Nielsen and Rikke Schmidt Kjærgaard), has penned 29 columns in the period of August 2010 to December 2012, covering broad topics such as salience, Gestalt principles, color, typography, negative space, layout, and data integration.


The announcement of the return of the column, together with its history and a description of me, the new author, are available at the Nature Methods methagora blog. Humor is kept by repeated reference to my now-dead-but-once-famous pet rat.

When it was A.C. Greyling's turn to speak at a debate in which Christopher Hitchens and Richard Dawkins already made their points, Greyling said

When one gets up to speak this late in a debate, one is a bit tempated to quote that Hungarian M.P. who after a long, long, long discussion in the parliament in Budapest stood up and said, "Everything has been said but not everybody said it yet." (watch on YouTube)

Indeed, this is quite how I feel after being offered to be the new author of Nature Methods Point of View column. Both Bang and Hitchens provide significant inspiration for me, so Greyling's words are particularly fitting.

To improve on the column is impossible. My challenge is to identify useful topics that have not yet been covered. I will be working closely with Nature Methods and Bang to ensure that the columns strike the right balance of topic, tone and timbre.

In 2013 the Points of View column spawned the Points of Significance column, which deals with statistics in biological science.

For the month of August 2013, the entire set of 35 columns is available for free.

2015 and beyond

The column continues to run, though no longer monthly.

A PDF eBook of the 38 Points of View articles published between August 2010 and February 2015 is now available at the Nature Shop for $7.99 under the title Visual strategies for biological data: the collected Points of View.


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
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
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
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
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
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
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.