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
Embrace me, surround me as the rush comes.Motorcycledrift deeper into the soundmore quotes

information: curious


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

2020 `\pi` day art and the piku


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.

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

The Outbreak Poems

Tue 24-03-2020

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.

Read the poems and learn what a piku is.

Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses

Tue 17-03-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first SARS-CoV-2 genome (MT019529) to be sequenced appears first on the poster.

Using Circos in Galaxy Australia Workshop

Wed 04-03-2020

A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Using Circos in Galaxy Australia workshop. (zoom)

Download workshop slides.

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).

Essence of Data Visualization in Bioinformatics Webinar

Thu 20-02-2020

My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Essence of Data Visualization in Bioinformatics webinar. (zoom)

Download webinar slides.

Markov models — training and evaluation of hidden Markov models

Thu 20-02-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Markov models — training and evaluation of hidden Markov models. (read)

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

Tue 28-01-2020

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Luke and Mayia wearing limited edition volunteer t-shirts. The pattern reproduces the human genome with chromosomes as spirals. (zoom)

As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Precisely engineered frame mounts of flow cells used to sequence genomes in our laboratory. (zoom)

Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The plaque at the back of one of the framed Illumina flow cell. This one has sequence from a patient's lymph node diagnosed with Burkitt's lymphoma. (zoom)


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