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
Safe, fallen down this way, I want to be just what I am.Cocteau Twinssafe at lastmore quotes

visualization: beautiful


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

2020 `\pi` day art and the piku


fun + amusement

Eggnauts — Engineers Launch Model Rockets at UBC

Jul 27 2005 | text and photos by Martin Krzywinski | After reading the UBC media release announcing that model rockets would be fired at UBC, I could not resist.

The contest was to launch a rocket at least 150m into the air with a payload of an egg and bottle of maple syrup. You guess it - the egg had to be returned back to earth in relative safety. I was first in line to see the egg carnage, which promised to be the best part of the show. Who wants to see whole eggs landing in relative safety anyway?

The first launch - missed

Not knowing exactly where the launch would be held (the media release said Thundebird Park - which is huge), I was hanging around at the center of the park hoping that smoke and cheers would guide me. Sure enough, at about 5:30 I heard a bang and a puff of smoke.

I found the launch platform - but unfortunately missed the first lift-off.

The second launch - just smokin'

I was well positioned with my camera for the second launch. After a few times being told to step even further back - so that I would not get egg on my face, I'm sure - I settled into a position that was both safe and a good lookout.

Unfortunately, from my vantage point I was shooting right into the sun, so the photos are a little bleached out. I also had the 24-70mm f/2.8L on my 20D so I couldn't get good reach. The photos here are 100% crops.

Shooting at 5 fps, I caught the first sign of the plume developing around the rocket as its engines ignited.

UBC rocket launch

After the second frame, the acceleration was rapid and the rocket lifted off to 2-3 m before my next frame.

UBC rocket launch

And it was on its way!

UBC rocket launch

And then it just kept going, and going and going. It finally disappeared travelling west. Nobody heard from the egg again.

UBC rocket launch UBC rocket launch UBC rocket launch

The third launch - it's ok, the car's just a rental

After the second launch I repositioned myself to face south, with the sun at my back. After the excitement of the egg launched into orbit, I could hardly anticipate what came next. I was in for a show so exciting that all remaining launches were promptly canceled. Read on.

Before the launch, I caught the engineers looking over their rocket. Handling it lovingly, they were making sure that the eggnaut and maple syrup were snuggly nestled into the payload canister.

UBC rocket launch

The tension was palpable. Would it launch? Would it reach 150m? Would the eggnaut return to tell the tale without cracking?

UBC rocket launch

Once again, the shutter flapped at 5 fps as the rocket took off. This time, I caught the start of the plume at just the right time and captured the rocket take off in the first few frames.

UBC rocket launch

The trip started solidly for our eggnaut. The launch was timely, and more importantly, the rocket was travelling vertically - upwards. Would the egg make a career out of it? Just as our hopes were rising, we realized that something was terribly wrong. Shortly after take off, it became clear that the eggnaut was doomed. We didn't want to believe it at first, but it was obvious that the flight plan was taking a turn for the worse.

UBC rocket launch

The rocket began to spin wildly. To add, it began to turn to traveling the directly of the shocked onlookers and the parking lot. It was not longer just about the egg anymore. Fear gripped me, but I kept shooting. The next four frames reveal the horrible events that sealed the eggnaut's doom. In the second of the frames, an unplanned explosion is clearly seen. The rocket is undeterred by this, and continues to fly in the direction of the spectators.

UBC rocket launch

UBC rocket launch

UBC rocket launch

UBC rocket launch

The travel path became more erratic, and only a few seconds later the last booster cut-off. The eggnaut, perhaps still viable, was in free fall. Falling, accelerating - right into the parking lot.

UBC rocket launch

I started running towards the extrapolated crash site, as I heard a thud. When I got there, a small crowd already formed around the impact site. Someone called for an eggdoctor. In my first shot of the macabre, only the parachute, never deployed, is seen. The true extent of the disaster is covered by the figure of solemn child.

UBC rocket launch

Rapidly, the team of engineers arrived on site. Although the rocket spent about 10 fateful seconds in the air, it only traveled about 30 meters, as the crow flies (which it does much longer).

UBC rocket launch

Of course, all eyes were on the contents. Was the eggnaut safe? Perhaps by some earthly miracle, the impact was not severe enough. Of course, even before the rocket payload canister was opened, we all knew that the sickly thud that placed the rocket less than a meter from a car was a mortal hit to our airborne friend.

UBC rocket launch

The next photo captures the human moment of tragedy. The team lead finally realizes that nothing survived. The man behind him and to the right bites his lip in disappointment and shock.

UBC rocket launch

The next photo reveals the payload - now turned into an ogrish paste of eggnaut and maple syrup.

UBC rocket launch

The fourth launch - canceled

The fourth team stood by - their launch canceled. Their hearts were heavy with the tragedy of the previous team's horrible flame-out. One of the team members is seen here so distraught that he kneals and leans on his rocket for support.

UBC rocket launch

Yet they could not help but imagine - how far would their eggnaut have traveled?

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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.

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