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a rat: exciting


Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca
The Outbreak Poems — artistic emissions in a pandemic


Alex — Internet's Most Popular Rat

Poster Rat for Rat Genome Sequencing

The rat genome sequencing project at the Baylor College of Medicine Human Genome Sequencing Centre is complete. The genome has been analyzed and published.

I'd like to introduce you one of the faces of the project: Alex, the genomics rat idol.

Arguably, Alex is the most popular rat on the internet. For the justification of this strong statement, read on.

rat (Rattus norvegicus) on genome sequencer - alex on an abi 3700 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Alex, the rat. Rattus norvegicus on an ABI 3700 genome sequencer. (zoom)
rat (rattus norvegicus) on genome sequencer - alex on an abi 3700 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Alex, the rat. Rattus norvegicus on an ABI 3700 genome sequencer. (zoom)

Alex's Biography

Alex was born in May 2000. It's well known that a rat's cuteness reaches maximum at about 3-4 weeks. After this critical time, a pet store rat is less likely to be purchased and may be asked to act as snake food. In Alex's case, she was perilously close to her deadline. Luckily for her, we paid a ransom of $6.99 to the Noah's Ark pet shop in Vancouver. She was on her last cute leg.

Portrait of Alex, the genome rat (Rattus norvegicus). / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Portrait of Alex, the genome rat (Rattus norvegicus). Here, she is seen in a forced portrait position (zoom)

From May 2000 Alex spent most of her time hoarding food pellets and riding on shoulders.

Portrait of Alex, the genome rat (Rattus norvegicus). Riding on shoulder. / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Portrait of Alex, the genome rat (Rattus norvegicus). Riding on shoulder.

Alex liked to bite. And rats only bite hard — they don't nibble. Her contention for this unattractive behaviour was the uncanny similarity between a finger and a pellet of food.

Other than unpredictable bouts of biting (by far the most exciting aspect of her personality), Alex lacked other distinguishing characteristics.

Alex died of a seizure in late 2002. She was buried outside of the Museum of Anthropology. A ratty pair of underwear served as a burial shroud.

And I hope you got that last pun.

DOWNLOAD ALL PHOTOS.

Photos are for public use. Use, modification and distribution of these photos is unrestricted.

Alex's Popularity

Despite my best efforts at meaningful work, this web page continues to be the most popular of all my online offerings, making for a somewhat embarrassing achievement.

Alex's images consistently show up first in Google's web search for 'rat', 'rat image' and image search for 'rat'.

Portrait of Alex, the genome rat (Rattus norvegicus). / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Alex image is the first for Google's 'rat' search query (retrieved 16 Mar 2013). (rat Google search)
Portrait of Alex, the genome rat (Rattus norvegicus). / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Alex image is the first for Google's 'rat image' search query (retrieved 16 Mar 2013). (rat Google search)

Finally, Alex appears as the first entry in Google images for 'rat'.

Portrait of Alex, the genome rat (Rattus norvegicus). / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Alex image is the first for Google's 'rat image' search query (retrieved 16 Mar 2013). (rat Google search)

Alex's Public Appearances

Alex is neither without modesty nor public fame. Her first cover-ratgirl appearance was on the April 2004 issue of Genome Research.

Rat Issue of Genome Research, April 2004 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Alex the rat appeared on the cover of Genome Research (April 2004). (zoom)

More recently, she's appeared on the cover of Ethnologie Francaise (Jan-Mar 2009 issue).

Alex the rat on the cover of Ethnologie Francaise (1/2009) / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Alex the rat appeared on the cover of Ethnologie Francaise (1/2009). (zoom)

The topic of the issue was the relationship between animals and humans. It is fitting therefore to recount here the relationship I shared with Alex during her sojourn with us.

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news + thoughts

Virus Mutations Reveal How COVID-19 Really Spread

Mon 04-05-2020

Genetic sequences of the coronavirus tell story of when the virus arrived in each country and where it came from.

Our graphic in Scientific American's Graphic Science section in the June 2020 issue shows a phylogenetic tree based on a snapshot of the data model from Nextstrain as of 31 March 2020.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Virus Mutations Reveal How COVID-19 Really Spread. Text by Mark Fischetti (Senior Editor), art direction by Jen Christiansen (Senior Graphics Editor), source: Nextstrain (enabled by data from GISAID).

Cover of Nature Cancer April 2020

Mon 27-04-2020

Our design on the cover of Nature Cancer's April 2020 issue shows mutation spectra of patients from the POG570 cohort of 570 individuals with advanced metastatic cancer.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Each ellipse system represents the mutation spectrum of an individual patient. Individual ellipses in the system correspond to the number of base changes in a given class and are layered by mutation count. Ellipse angle is controlled by the proportion of mutations in a class within the sample and its size is determined by a sigmoid mapping of mutation count scaled within the layer. The opacity of each system represents the duration since the diagnosis of advanced disease. (read more)

The cover design accompanies our report in the issue Pleasance, E., Titmuss, E., Williamson, L. et al. (2020) Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer 1:452–468.

Modeling infectious epidemics

Wed 06-05-2020

Every day sadder and sadder news of its increase. In the City died this week 7496; and of them, 6102 of the plague. But it is feared that the true number of the dead this week is near 10,000 ....
—Samuel Pepys, 1665

This month, we begin a series of columns on epidemiological models. We start with the basic SIR model, which models the spread of an infection between three groups in a population: susceptible, infected and recovered.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

We discuss conditions under which an outbreak occurs, estimates of spread characteristics and the effects that mitigation can play on disease trajectories. We show the trends that arise when "flattenting the curve" by decreasing `R_0`.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

This column has an interactive supplemental component that allows you to explore how the model curves change with parameters such as infectious period, basic reproduction number and vaccination level.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.