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Poetry is just the evidence of life. If your life is burning well, poetry is just the ashLeonard Cohenburn somethingmore quotes
activities

I present clearly, connect broadly, spark imagination and encourage enthusiasm for inquiry. I create visuals with analytical clarity and artistic dimensions.

In 1999 I built the Genome Sciences Centre's first computing systems, and later invented port knocking, and optimized keyboard layouts that spawned a Brazilian fashion line. I have an affinity for parody and tragedy. I love rabbit holes.

I created Circos (a community standard) and hive plots (a farewell to hairballs). I am triggered by slipshod visualizations of science and pie charts.

My information graphics have appeared in the New York Times, Wired, and on covers of books and scientific journals such as Science, Nature and PNAS.

I am a co-author of the Nature Methods Points of Significance and Points of View columns. I contribute to Scientific American's Graphic Science and teach how to design scientific figures and scientific posters. My method is critique by redesign.

I’ve made maps of nothings in the Universe, shot fashion photography, found poems in spam. Every year I make Pi Day art, which can be graphics, words or music. I made a music video about infinity, I love typography and run Hitchmas.

I am a former owner of Alex, the world’s most popular rat.

contact

Martin Krzywinski

Staff Scientist

Canada's Michael Smith Genome Sciences Centre

570 West 7th Avenue

Vancouver BC

V5Z 4S6

Canada

main activities
Circos
Deadly genomes
Graphic Science
Hive plots
Journal covers
Nature Methods Points of Significance
Nature Methods Points of View
Pi Day
Typography
journal covers
Cover of Cell Genomics 2023
Cover of Science Advances 2023
Cover of Nature 2022
Cover of Cancer Cell 2022
Cover of PNAS 2022
Cover of Annals of Oncology 2022
Cover of Nature Biotechnology 2022
Cover of Science 2021
Cover of Nature Genetics 2020
Cover of Nature Cancer 2020
Cover of Molecular Case Studies 2018
Cover of Nature 2017
Cover of PNAS 2012
Cover of Trends in Genetics 2012
Cover of Genome Research 2012
Cover of Genome Informatics 2010
Cover contest for EMBO journal
Cover of EMBO Journal 2009
Cover of American Scientist 2007
Pi Day Art
2023 Pi Day — Repeated Sequence
2022 Pi Day — three one four: a number of notes
2021 Pi Day - Forest of Digits
2020 Pi Day — Piku
2019 Pi Day — Languages
2018 Tau Day
2018 Pi Day — Bringing the world together
2017 Pi Day — Pi in the sky
2016 Pi Day — Gravity of Pi
2015 Pi Day — Transcendental map
2014 Pi Day — Frequency circles
2013 Pi Day — It stars here
Three one four: a number of notes
other activities
16 and's — typographical peep show
5 years of personalized cancer care
Adobe swatches for Brewer palettes
Alex — Internet's most popular rat
ASCII art
Bird song mnemonics
CARPALX - keyboard layouts and Brazilian fashion
Circos online tableviewer
Color proportions in your image
Color resources
The COVID charts
Dinosaurs of the corn - fixing visualizations
DNA on 10th wayfinding
Dummer — a Hummer parody
e.e. spammings
Essentials of Data Visualization — 8-part video series
Eye charts — a modern interpretation
Flunk — Down Here / Moon Above — Music for space
Gene Machines — Vinyl sounds from the lab
Genomics 3D art exhibit
Gigapixel 1-bit Moon, Solar System & Sky
Google maps longest routes
Graphical abstract design
High dynamic time range photography
Hilbert curves and Hilbertonians
History of the human genome assembly
Hitchmas
Hitchsum — Hitchens ipsum
Languages on the globe
LOTRO — Warden gambit chart
Lumondo photography
Max Cooper — Aleph 2 — Music for minds
Max Cooper — Ascent — Music for dimensions
MIT Museum genome exhibit
The Outbreak Poems
Poster design guidelines
Proportions of colors in country flags
Ptolemaic clock
Quotes archive
SARS-CoV-2 visualizations of 56 genomes
Scientific American Graphic Science
Snellen optotype font
snowflake catalogue — in silico flurries
Tripsum — Trump ipsum
UBC rocket contest
Universe — superclusters and voids
Unwords — what's missing in the English language
Visions of type — type peep show
Weightlifting socks - 178.75 lb
Word analysis of 2008–2020 U.S. Presidential Debates
World's most popular questions
Writing
Yes or No
Zen and the Art of Motorcycle Maintenance quotes
buy artwork Song of the Barred Owl (Strix varia) by Martin Krzywinski
SCIENCE + ART | Put it on your wall. (buy artwork / see all my art)
very clickable

projects

Circos

Circos is software that generates circularly composited views of genomic data and annotations.

Circos - Circular Genome Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circos is a tool for visualizing data in a circular layout. It is widely used in genomics and cancer biology, but can show any kind of data. (Learn more)

Figures created by Circos are engaging, pretty and informative.

Circos - Circular Genome Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Many kind of data tracks are supported. Shown here is a small sample: links, tiles and heatmaps. (Learn more)

Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. (presentations on Circos; drawn heavily from Tufte's Visual Display of Quantitative Information)

Circos - Circular Genome Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Data display can be automated to show a large number of tracks. (Learn more)

RESOURCES

Circos - Circular Genome Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Talks on Circos and its uses.

Circos - Circular Genome Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circos course.

Circos - Circular Genome Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circos in the literature.

Hive Plots

Hive plots are a type of layout algorithm that is designed to make sense out of very large networks. The method is quantitative — placement of nodes depends only on network properties.

Hive Plots - Rational Network Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
In a hive plot, nodes are placed on linear axes, which are arranged radially. Nodes are mapped to axis based on topology (e.g. connectivity) or user categories. Network edges are shown as links between axis node points, and can be colored further by additional metadata.

Hive plots are an answer to the challenge of uninformative network hairball visualization.

Hive Plots - Rational Network Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
In a hive plot, nodes are placed on linear axes, which are arranged radially. Nodes are mapped to axis based on topology (e.g. connectivity) or user categories. Network edges are shown as links between axis node points, and can be colored further by additional metadata.

Hive Plots - Rational Network Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hive plots are excellent at showing alignments between more than two genomes. (High resolution on white or black)

Hive Plots - Rational Network Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hive plots are excellent at comparing ratios. Here each panel shows 24 ratios (8 between each axis pair).

RESOURCES

Hive Plots - Rational Network Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
VIZBI 2011 Hive Plot Poster.

Hive Plots - Rational Network Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Introduction to hive plots.

Hive Plots - Rational Network Visualization / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genome Informatics 2010 talk.

Genome Informatics Cover

I had the opportunity to design the cover of the Genome Informatics Conference program book. The cover shows sequences of some of the genes and viruses that appear in this conference's abstracts and uses the genome path algorithm previously used in the Deadly Genomes poster.

Read the details about the design.

Cover of Genome Informatics 2010 Program

Cover of Genome Informatics 2010 Program

Deadly Genomes — Run Away

The Deadly Genomes is a visualization of the size and structure of genomes of viruses and bacteria that are agents of prevalent human diseases. Their genomes are visualized as a path, and each organism is spaced on the poster according to the incidence and mortality of the disease.

The Deadly Genomes - Size and Structure of Deadly Viruses and Bacteria

This image reached the finalist stage at the 2009 National Science Foundation Visualization Challenge.


Our 10 year anniversary

December 2009 saw the 10th Anniversary of the Genome Sciences Center. Some commemorative swag was handed out, among which was a stainless steel water bottle with the following image.

Genome Sciences Center 10th Anniversary Commemorative Graphic - QR Code

The image contains a barcode called QR Code (learn more) which encodes the names of all current employees at the Center.

Visualizing Debates

Lexical analysis of 2008 US Presidential and Vice-Presidential Debates indicates that the speech patterns between candidates (especially those paired in a debate) are extremely similar and that the complexity of vice-presidential candidates is lower than presidential candidates (uniqueness is lower, repetition is higher).

Palin has the longest sentences, Biden repeats himself the most and has the smallest vocabulary, while patterns for Obama and McCain are eerily similar.

Use Atom feeds of candidates' word lists to create Wordles.


Optimizing Keyboard Layouts - carpalx

carpalx - keyboard layout optimizer

carpalx is a keyboard optimizer which rearranges letter positions on a keyboard to minimize typing effort. Discover the magical XBUL keyboard layouts which minimizes typing of English text. Or, if you dare, venture into the land of the disfigured TNWCLR keyboard layout which makes typing English text excruciatingly painful.

High Dynamic Time Range Photography (HDTR)

High Dynamic Time Range images (HDTR) are single-frame composites of a set of time-lapse photos.


Perl Workshops

The bioinformatics Perl workshop offers courses to help you learn Perl and apply it to your work. We have courses on introductory Perl, intermediate Perl, and others. Learn how to use map, grep and sort more efficiently or how to perform data analysis at the command line. The workshop is open to the public (given at the GSC 570 W 7th location) and all slides from each lecture are available online.

schemaball

schemaball generates circularly composited views of SQL database schemas


BAC Arrays


High-resolution 32k BAC array for aCGH studies of human genome.

clusterpunch

clusterpunch is a mini-benchmarker for clusters designed to monitor availability of resources


port knocking

portknocking is a network authentication method in which a client establishes a connection to a host which presents no open ports

Life of Alex

alex is a very famous pet rat, who had appearances in Genome Research and Maximum PC.


Tuple Color Encoding

color encoding of vectors Color::TupleEncode - Mapping tuples to colors and visually comparing numbers

Yes or No

yesorno (get answers to your problems - just answers)


Genome Coverage Tables

short-read sequencing genome coverage tables tables of read coverage for haploid, diploid and triploid genomes for a given sequencing redundancy

genome coverage simulator explore whole genome shotgun statistics


Image Color Summarizer

Image color summarizer produces statistics about an image's mean/median hue, saturation and intensity values. It's fun to play with and can be (eventually) used to auto-tag images based on color content.


Lumondo Photography

Lumondo Photography is my commercial front-end.

Canon Lenses

Canon EF Lenses A f/ vs mm chart of all Canon EF lenses, and a few links to useful lens resources.


UBC Rockets

UBC model rocket launch competition was not without accidents.

Visualizing an MMRPG Class

I am a warden.


news + thoughts

Neural network primer

Mon 06-02-2023

Nature is often hidden, sometimes overcome, seldom extinguished. —Francis Bacon

In the first of a series of columns about neural networks, we introduce them with an intuitive approach that draws from our discussion about logistic regression.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Neural network primer. (read)

Simple neural networks are just a chain of linear regressions. And, although neural network models can get very complicated, their essence can be understood in terms of relatively basic principles.

We show how neural network components (neurons) can be arranged in the network and discuss the ideas of hidden layers. Using a simple data set we show how even a 3-neuron neural network can already model relatively complicated data patterns.

Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20.

Background reading

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

Cell Genomics cover

Mon 16-01-2023

Our cover on the 11 January 2023 Cell Genomics issue depicts the process of determining the parent-of-origin using differential methylation of alleles at imprinted regions (iDMRs) is imagined as a circuit.

Designed in collaboration with with Carlos Urzua.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Our Cell Genomics cover depicts parent-of-origin assignment as a circuit (volume 3, issue 1, 11 January 2023). (more)

Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq (2023) Cell Genomics 3(1).

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Science Advances cover

Thu 05-01-2023

My cover design on the 6 January 2023 Science Advances issue depicts DNA sequencing read translation in high-dimensional space. The image showss 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes.

More details about the design.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Science Advances cover that encodes sequence onto hypercubes (volume 9, issue 1, 6 January 2023). (more)

Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9.

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Regression modeling of time-to-event data with censoring

Mon 21-11-2022

If you sit on the sofa for your entire life, you’re running a higher risk of getting heart disease and cancer. —Alex Honnold, American rock climber

In a follow-up to our Survival analysis — time-to-event data and censoring article, we look at how regression can be used to account for additional risk factors in survival analysis.

We explore accelerated failure time regression (AFTR) and the Cox Proportional Hazards model (Cox PH).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Regression modeling of time-to-event data with censoring. (read)

Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Regression modeling of time-to-event data with censoring. Nature Methods 19.

Music video for Max Cooper's Ascent

Tue 25-10-2022

My 5-dimensional animation sets the visual stage for Max Cooper's Ascent from the album Unspoken Words. I have previously collaborated with Max on telling a story about infinity for his Yearning for the Infinite album.

I provide a walkthrough the video, describe the animation system I created to generate the frames, and show you all the keyframes

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Frame 4897 from the music video of Max Cooper's Asent.

The video recently premiered on YouTube.

Renders of the full scene are available as NFTs.

Gene Cultures exhibit — art at the MIT Museum

Tue 25-10-2022

I am more than my genome and my genome is more than me.

The MIT Museum reopened at its new location on 2nd October 2022. The new Gene Cultures exhibit featured my visualization of the human genome, which walks through the size and organization of the genome and some of the important structures.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My art at the MIT Museum Gene Cultures exhibit tells shows the scale and structure of the human genome. Pay no attention to the pink chicken.
I value
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

© 1999–2023 Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA