resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
biography · poster · CV
SPP / Cambridge, UK / Nov 2019
Staff Scientist
Canada's Michael Smith Genome Sciences Centre at BC Cancer
570 W 7th Avenue
Vancouver BC
V5Z 4S6 Canada
martink@bcgsc.ca
@mkrzywinski
activities
With some very smart people, I work on problems in data visualization applied to cancer research and genome analysis. Previously I was involved in fingerprint mapping, system administration, computer security, fashion photography, medical imaging and LHC particle physics. My work is guided by a need to rationalize, make things pretty, combine science with art, mince words, find good questions and help make connections between ideas. All while exercising snark.
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.
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.
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.
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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.
Panic can wait for tomorrow.
Regrets live on curves not tangents.
Small chances are never zero.
Month's last day waits for another year.
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.
I value
