Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
Poetry is just the evidence of life. If your life is burning well, poetry is just the ashLeonard Cohenburn somethingmore quotes

Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca

2020 `\pi` day art and the piku


statistics + data

Nature Methods: Points of Significance

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Points of Significance column in Nature Methods. (Launch of Points of Significance)
47 | Grewal, J., Krzywinski, M. & Altman, N. (2020) Points of significance: Markov models — training and evaluation of hidden Markov models. Nature Methods 17:121–122.
46 | Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Hidden Markov models. Nature Methods 16:795–796.
45 | Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Markov chains. Nature Methods 16:663–664.
44 | Das, K., Krzywinski, M. & Altman, N. (2019) Points of significance: Quantile regression. Nature Methods 16:451–452.
43 | Greco, L., Luta, G., Krzywinski, M. & Altman, N. (2019) Points of significance: Analyzing outliers: Robust methods to the rescue. Nature Methods 16:275–276.
42 | Smucker, B., Krzywinski, M. & Altman, N. (2019) Points of significance: Two-level factorial experiments Nature Methods 16:211–212.
41 | Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.
40 | Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design Nature Methods 15:559–560.
39 | Altman, N. & Krzywinski, M. (2018) Points of significance: Curse(s) of dimensionality Nature Methods 15:299–400.
38 | Bzdok, D., Krzywinski, M. & Altman, N. (2018) Points of significance: Statistics vs machine learning. Nature Methods 15:233–234.
37 | Bzdok, D., Krzywinski, M. & Altman, N. (2018) Points of significance: Machine learning: supervised methods. Nature Methods 15:5–6.
36 | Bzdok, D., Krzywinski, M. & Altman, N. (2017) Points of significance: Machine learning: a primer. Nature Methods 14:1119–1120.
35 | Altman, N. & Krzywinski, M. (2017) Points of significance: Ensemble methods: Bagging and random forests. Nature Methods 14:933–934.
34 | Krzywinski, M. & Altman, N. (2017) Points of significance: Classification and regression trees. Nature Methods 14:757–758.
33 | Lever, J., Krzywinski, M. & Altman, N. (2017) Points of significance: Principal component analysis. Nature Methods 14:641–642.
32 | Altman, N. & Krzywinski, M. (2017) Points of significance: Clustering. Nature Methods 14:545–546.
31 | Altman, N. & Krzywinski, M. (2017) Points of significance: Tabular data. Nature Methods 14:329–330.
30 | Altman, N. & Krzywinski, M. (2017) Points of significance: Interpreting P values. Nature Methods 14:213–214.
29 | Altman, N. & Krzywinski, M. (2017) Points of significance: P values and the search for significance. Nature Methods 14:3–4.
28 | Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Regularization. Nature Methods 13:803–804.
27 | Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Model selection and overfitting. Nature Methods 13:703–704.
26 | Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Classifier evaluation. Nature Methods 13:603–604.
25 | Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.
24 | Altman, N. & Krzywinski, M. (2016) Points of significance: Regression diagnostics. Nature Methods 13:385–386.
23 | Altman, N. & Krzywinski, M. (2016) Points of significance: Analyzing outliers: Influential or nuisance. Nature Methods 13:281–282.
22 | Krzywinski, M. & Altman, N. (2015) Points of significance: Multiple linear regression. Nature Methods 12:1103–1104.
21 | Altman, N. & Krzywinski, M. (2015) Points of significance: Simple linear regression. Nature Methods 12:999–1000.
20 | Altman, N. & Krzywinski, M. (2015) Points of significance: Association, correlation and causation. Nature Methods 12:899–900.
19 | Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of significance: Bayesian networks. Nature Methods 12:799–800.
18 | Kulesa, A., Krzywinski, M., Blainey, P. & Altman, N. (2015) Points of significance: Sampling distributions and the bootstrap. Nature Methods 12:477–478.
17 | Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of significance: Bayesian statistics. Nature Methods 12:277–278.
16 | Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of significance: Bayes' theorem. Nature Methods 12:277–278.
15 | Altman, N. & Krzywinski, M. (2015) Points of significance: Split plot design. Nature Methods 12:165–166.
14 | Altman, N. & Krzywinski, M. (2015) Points of significance: Sources of variation. Nature Methods 12:5–6.
13 | Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.
12 | Krzywinski, M., Altman, N. & Blainey, P. (2014) Points of significance: Nested designs. Nature Methods 11:977–978.
11 | Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of significance: Replication. Nature Methods 11:879–880.
10 | Krzywinski, M. & Altman, N. (2014) Points of significance: Analysis of variance (ANOVA) and blocking. Nature Methods 11:699–700.
9 | Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments. Nature Methods 11:597–598.
8 | Krzywinski, M. & Altman, N. (2014) Points of significance: Non-parametric tests. Nature Methods 11:467–468.
7 | Krzywinski, M. & Altman, N. (2014) Points of significance: Comparing samples — Part II — Multiple testing. Nature Methods 11:355–356.
6 | Krzywinski, M. & Altman, N. (2014) Points of significance: Comparing samples — Part I — t–tests. Nature Methods 11:215–216.
5 | Krzywinski, M. & Altman, N. (2014) Points of significance: Visualizing samples with box plots. Nature Methods 11:119–120.
4 | Krzywinski, M. & Altman, N. (2013) Points of significance: Power and sample size. Nature Methods 10:1139–1140.
3 | Krzywinski, M. & Altman, N. (2013) Points of significance: Significance, P values and t–tests. Nature Methods 10:1041–1042.
2 | Krzywinski, M. & Altman, N. (2013) Points of significance: Error bars. Nature Methods 10:921–922.
1 | Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.

VIEW ALL

news + thoughts

The Outbreak Poems

Tue 24-03-2020

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.

Read the poems and learn what a piku is.

Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses

Tue 17-03-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first SARS-CoV-2 genome (MT019529) to be sequenced appears first on the poster.

Using Circos in Galaxy Australia Workshop

Wed 04-03-2020

A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. 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.