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.
projects
Circos
Circos is software that generates circularly composited views of genomic data and annotations.
Figures created by Circos are engaging, pretty and informative.
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)
RESOURCES
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 are an answer to the challenge of uninformative network hairball visualization.
RESOURCES
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.
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.
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.
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 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.
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
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
Typography
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.
Flickr stream
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.
Visualizing an MMRPG Class
VIEW ALL
news + thoughts
Standardization fallacy
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.
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
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.
"This data might give you a migrane"
An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.
He said, he said — a word analysis of the 2020 Presidential Debates
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.
Points of Significance celebrates 50th column
We are celebrating the publication of our 50th column!
To all our coauthors — thank you and see you in the next column!
Uncertainty and the management of epidemics
When modelling epidemics, some uncertainties matter more than others.
Public health policy is always hampered by uncertainty. During a novel outbreak, nearly everything will be uncertain: the mode of transmission, the duration and population variability of latency, infection and protective immunity and, critically, whether the outbreak will fade out or turn into a major epidemic.
The uncertainty may be structural (which model?), parametric (what is `R_0`?), and/or operational (how well do masks work?).
This month, we continue our exploration of epidemiological models and look at how uncertainty affects forecasts of disease dynamics and optimization of intervention strategies.
We show how the impact of the uncertainty on any choice in strategy can be expressed using the Expected Value of Perfect Information (EVPI), which is the potential improvement in outcomes that could be obtained if the uncertainty is resolved before making a decision on the intervention strategy. In other words, by how much could we potentially increase effectiveness of our choice (e.g. lowering total disease burden) if we knew which model best reflects reality?
This column has an interactive supplemental component (download code) that allows you to explore the impact of uncertainty in `R_0` and immunity duration on timing and size of epidemic waves and the total burden of the outbreak and calculate EVPI for various outbreak models and scenarios.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Uncertainty and the management of epidemics. Nature Methods 17.
Background reading
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.
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