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
The Outbreak Poems
I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.
Thoughts crack through night to a still clock.
Clogged channels stuck with nervous silt.
Song to sleep and poem to wake to.
Once in a while a long moment.
Lump on head from hole in stomach.
Universe of no mind but ours.
Higher than birds stars glide at night.
Sleeps or hides some thing internal.
Pieces move by rules not yet written.
Clouds visit then as fog they stay.
Distant duck bobs like something else.
Not above the belows but in them.
Yesterday comes by starlight to day.
It's always not now somewhere else.
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
