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
Twenty — minutes — maybe — more.Naomichoose four wordsmore quotes

visualization: curious


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

Scientific graphical abstracts — design guidelines


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.


VIEW ALL

news + thoughts

Happy 2021 `\pi` Day—
A forest of digits

Sun 14-03-2021

Celebrate `\pi` Day (March 14th) and finally see the digits through the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 26th tree in the digit forest of `\pi`. Why is there a flower on the ground?. (details)

This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first 46 digits of `\pi` in 8 trees. There are so many more. (details)

And things can get crazy in the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A forest of the digits of '\pi`, by ecosystem. (details)

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, 2018 `\pi` Day and 2019 `\pi` Day.

Testing for rare conditions

Tue 16-03-2021

All that glitters is not gold. —W. Shakespeare

The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.

We discuss the positive predictive value (PPV) and how practices such as screen can increase it.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Testing for rare conditions. (read)

Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18

Standardization fallacy

Tue 09-02-2021

We demand rigidly defined areas of doubt and uncertainty! —D. Adams

A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.

Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Standardization fallacy. (read)

Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.

Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.

Graphical Abstract Design Guidelines

Fri 13-11-2020

Clear, concise, legible and compelling.

Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.

"This data might give you a migrane"

Tue 06-10-2020

An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A poster of high BMI and obesity prevalence for 185 countries.

He said, he said — a word analysis of the 2020 Presidential Debates

Thu 01-10-2020

Building on the method I used to analyze the 2008, 2012 and 2016 U.S. Presidential and Vice Presidential debates, I explore word usagein the 2020 Debates between Donald Trump and Joe Biden.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Analysis of word usage by parts of speech for Trump and Biden reveals insight into each candidate.


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