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celebration: let's do it again


Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca
2020 `\pi` day art and the piku


data visualization + celebration

Genome Sciences Center 20th Anniversary Clothing, Music, Drinks and Art

On 15 November 2019, the Genome Sciences Center held its 20th anniversary celebration.

Here you can read about the design of the evening's clothing, music, drinks and other art.

After silence, that which comes nearest to expressing the inexpressible is music.
— Aldous Huxley

Music

We commissioned Segue to create a unique ambient music landscape for the celebration.

Segue is the name used by Jordan Sauer, an electronic music producer from Vancouver, BC. He creates ambient electronic music with layers of field recordings, acoustic and electronic sounds, creating sonic soundscapes that conjure images of nature and emotions of peace and introspection. He has release numerous solo albums and collaborations with artists from around the world, and recently released a solo album “The Island” on the Silent Season record label in summer 2019. Jordan is thrilled to partner with the GSC in the production of “Gene Machines”.

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ambient music performance by Segue (Jordan Sauer). (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ambient music performance by Segue (Jordan Sauer). (zoom)

gene machines

Gene machines will be available as a digital download soon. We are also planning to have a vinyl release.

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Gene Machines by Segue (Jordan Sauer). (zoom)

An assembly of shifting soundscapes, textures and rhythmic loops produced by the laboratory machines.

In commemoration of the 20th anniversary of Canada’s Michael Smith Genome Sciences Centre, Segue was comissioned to create an original composition based on audio recordings from the GSC’s laboratory equipment, robots and computers—to make “music” from the noise they produce.

Machine noise is a challenging palette of musical ingredients—sharp, abrasive and whirring sounds are typically unpleasant. For one night, these machines are repurposed as acoustical performers.

In the process of creating “Gene Machines”, recordings were analyzed for their specific frequency profiles and then used to generate melodic or percussive sounds. Together with bass from a Moog synthesizer, the sounds were then stretched, manipulated and sequenced into a series of compositions. Each composition is based on the recording from one specific laboratory machine, emphasizing its tone and timbre quality.

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Early version of the liner notes for Gene Machines by Segue. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Early version of the liner notes for Gene Machines by Segue. (zoom)

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Early version of the liner notes for Gene Machines by Segue. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Early version of the liner notes for Gene Machines by Segue. (zoom)

BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Early version of the liner notes for Gene Machines by Segue. (zoom)
BC Cancer Genome Sciences Center 20th Anniversary Celebration / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Early version of the liner notes for Gene Machines by Segue. (zoom)

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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.

Panic can
wait
for tomorrow.
Regrets live
on
curves not tangents.
Small chances
are
never zero.
Month's last day
waits
for another
year.

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)