resources
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lunch break
Distractions and amusements, with a sandwich and coffee.
Alex — Internet's Most Popular Rat
Poster Rat for Rat Genome Sequencing
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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. 
▲ Alex, the rat. Rattus norvegicus on an ABI 3700 genome sequencer.
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▲ Alex, the rat. Rattus norvegicus on an ABI 3700 genome sequencer.
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Alex's BiographyAlex 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). Here, she is seen in a forced portrait position
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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.
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 PopularityDespite 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'. 
▲ Alex image is the first for Google's 'rat' search query (retrieved 16 Mar 2013).
(rat Google search)
▲ 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'. 
▲ Alex image is the first for Google's 'rat image' search query (retrieved 16 Mar 2013).
(rat Google search)
Alex's Public AppearancesAlex is neither without modesty nor public fame. Her first cover-ratgirl appearance was on the April 2004 issue of Genome Research. 
▲ Alex the rat appeared on the cover of Genome Research (April 2004).
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More recently, she's appeared on the cover of Ethnologie Francaise (Jan-Mar 2009 issue). 
▲ Alex the rat appeared on the cover of Ethnologie Francaise (1/2009).
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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. |
news + thoughts
Predicting with confidence and tolerance
I abhor averages. I like the individual case. —J.D. Brandeis.We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.
Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).
Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.
Background reading
Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.
4-day Circos course
A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.
Oryza longistaminata genome cake
Data visualization should be informative and, where possible, tasty.
Stefan Reuscher from Bioscience and Biotechnology Center at Nagoya University celebrates a publication with a Circos cake.
The cake shows an overview of a de-novo assembled genome of a wild rice species Oryza longistaminata.
