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.
The commemorative 10th anniversary image is a two-dimensional barcode.
Similar to the kinds used in our lab, this large-capacity barcode format was
created in Japan, where it has become a meme for transmission of
personal information. The code is called QR Code and it can encode up
to 2,953 alphanumeric characters.
The QR Code has been used by the Pet Shop Boys for the artwork of the cover of their Integral single. The image on the album encodes the address ofthe group's website, petshopboys.co.uk.
The code's high capacity allowed us to generate a commemorative graphic. The graphic's content stores the full names of all present GSC employees, a link to our web site and a timestamp. To convert the dots to text and extract the content submit the barcode image to the online decoder.
You can generate QR codes and buy labeled products here.
>> by Martin Krzywinski and Stephanie McInnis
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news + thoughts
The Outbreak Poems
I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.
Panic can wait for tomorrow.
Regrets live on curves not tangents.
Small chances are never zero.
Month's last day waits for another year.
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
