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
What do the trees know.Lalehsway, sway, swaymore quotes

visualization: beautiful


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

2020 `\pi` day art and the piku


fun + amusement

Dummer - Like Nothing Else / A Hummer Satire

The Dummer project might give you the impression that I don't like Hummers. You'd be right.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
What's after worst? This. (Dummer. Like nothing else.)

The project was well received by The New York Times and very poorly by someone who felt sending me hate mail was a good idea. It was — I loved it.

Other Hummer satires include fuh2.com — there's some hope for us all.


The World's Most Popular Questions

What are the world's most popular questions? After all, what we know defines us as much as what we ask. So, let's look at who we are.

Using Google's autocomplete feature, which suggests the most similar searches to the one you have entered, I maintain a real-time compilation of the most common questions asked by millions of worldwide internet users.

This project (a) yields insight into the zeitgeist and (b) scares me. My reason for fright are questions such as these:

General Issues

How do people do extreme couponing?

Why can't I hold all these limes?

Why do I always feel like murdering everyone?

What's up with the World

Is the world really flat?

is the world being controlled by aliens?

Limits & Desires

What happens if I make a formal commitment to Satan?

Love & Heart

Why is my boyfriend so insecure?

Why is my girlfriend so emotional?

Health

My head is full of pretty lumps.

Pain & Suffering

my elbow is dark and dry

why do I continue to hit myself with a hammer?

when does my head stop growing?

Sizes & Extremes

Who is the most powerful Jedi?

Where is the hardest part of your head?

Religion & Faith

Can Jesus microwave a burrito?

Can I pray with my eyes open?

Should I pray for a husband?

Neologisms - New Words, Much Needed

I like words. The pleasure of effectively using acerebral and defenestrate in the same sentence cannot be understated.

On occassion I found myself in a situation where no word fit, existing or that I know about. Instead of rushing to the dictionary, I decided to make up my own, such as inconversible (a statement without a logical converse), mystific (unexplainably wonderful), postpetizer (course ordered after dessert), prenopsis (a summary of something formulated before it was experienced), suscitate (breathe life into, for the first time), and others.

The current list of my neologisms is circos plot, compure, culturally inconversible, dependers, ee spammings, existangsty, fezday, hilbertonian, hive panel, hive plot, inconversible, metaomome, mystific, naytheism, naytheist, nes, neuroterror, neuroterrorism, newgrade, noward, nonposter, oldgrade, omome, omeomics, omicsophy, over, piddle, port knocking, postpetizer, pregratulate, prekfast, prenopsis, prepetizer, quinty, ratio hive, spammings, suscitate, unappropriate .


HDTR: High Dynamic Time Range Photography - Visualizing the Flow of Time

The HDTR method is a new approach to depicting the passage of time. High Dynamic Time Range (HDTR) images and are a composite of many photos taken over a long period of time, such as a day or even longer. Each part of the HDTR image is sampled from a different photo, either by column or row.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An HDTR is generated from a set of time-lapse images. Here, a simple HDTR is created from 5 images taken at different times. From each image, a strip representing 20% of the image is extracted and the strips are blended to reduce banding artefacts. (hires)

For example, the left part of the HDTR image might show the scene from 7am and the very right from 8pm, capturing the variation in light across an entire day.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An HDTR image shows the flow of time across a scene. Here the Vancouver skyline is shown from about 6pm (left) to 9pm (right). (Download)

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)


me as a keyword list

aikido | analogies | animals | astronomy | comfortable silence | cosmology | dorothy parker | drumming | espresso | fundamental forces | good kerning | graphic design | humanism | humour | jean michel jarre | kayaking | latin | little fluffy clouds | lord of the rings | mathematics | negative space | nuance | perceptual color palettes | philosophy of science | photography | physical constants | physics | poetry | pon farr | reason | rhythm | richard feynman | science | secularism | swing | symmetry and its breaking | technology | things that make me go hmmm | typography | unix | victoria arduino | wine | words