Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
Trance opera.Spente le Stelle

More than Pretty Pictures—Aesthetics of Data Representation, Denmark, April 13–16, 2015


fun + amusement

Neologisms - New Words

Creating new words is fun. It exercises the mind and adds a playful dimension to prosaic speech, without succumbing to bombast associated with deployment of arcane (and often lengthy) words.

When one's own neologisms are heard in use by other people, it also exercises the ego.

Word circulation status: accepted circos plot Word circulation status: new com·pure Word circulation status: new culturally inconversible Word circulation status: new de·pen·ders Word circulation status: new ee spammings Word circulation status: new ex·ist·angs·ty Word circulation status: new fez·day Word circulation status: new hil·ber·ton·ian Word circulation status: low hive panel Word circulation status: high hive plot Word circulation status: new in·con·ver·si·ble Word circulation status: low meta·om·ome Word circulation status: new mys·ti·fic Word circulation status: new nay·the·ism Word circulation status: new nay·the·ist Word circulation status: new nes Word circulation status: new neu·ro·ter·ror Word circulation status: new neu·ro·ter·ror·ism Word circulation status: new non·post·er Word circulation status: accepted om·ome Word circulation status: accepted ome·om·ics Word circulation status: new omic·so·phy Word circulation status: new over Word circulation status: new pid·dle Word circulation status: accepted port knocking Word circulation status: new post·pe·ti·zer Word circulation status: new pre·kfast Word circulation status: new pre·nop·sis Word circulation status: new pre·pe·ti·zer Word circulation status: new quin·ty Word circulation status: low ratio hive Word circulation status: new spammings Word circulation status: new sus·ci·tate

circulation level Neologism circulation level new new Neologism circulation level low low Neologism circulation level medium medium Neologism circulation level high high Neologism circulation level accepted accepted

Word circulation status: accepted circos plot noun

1a circularly arranged visualization created using Circos

2any circular visualization with concentric tracks, and especially those using lines or curves connecting points on the circumference usage of circos plot: "Genome visualization without Circos is like a fish with a bicycle." origin of circos plot: Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645

Word circulation status: new com·pure adjective

1having desirable qualities, often emphasizing visual qualities, so overly maximized as to be disfunctional or unuseable

2perfectly secure, but practically unusable, by virtue of physical and electronic isolation

3anything that is only great on paper usage of compure: "The IT department built us a compure network. Unfortunately, nobody can log on." usage of compure: "The apartment was compure—easy on the eyes but we couldn't figure out how to open the cupboards." usage of compure: "Beautiful and dumb, she was truly compure." origin of compure: computer + pure

Word circulation status: new culturally inconversible adjective

1a statement which is not strictly inconversible, but due to cultural or social constraints and customs, is practically so because uttering its converse would invite disgrace usage of culturally inconversible: "Politicians habitually employ cultural inconversibles to position themselves safely in the eyes of the public." example of culturally inconversible: "Men and women should be treated equally." see also: inconversible

Word circulation status: new de·pen·ders noun

1suspenders, discreetly worn under clothing, designed to hold up adult incontinence briefs or any other pads, guards and absorbency products

2suspenders worn under clothing usage of dependers: "Bob's dependers ensured him with not only peace of mind but also a snug and comfortable fit." origin of dependers: Depend + suspenders

Word circulation status: new ee spammings noun

1spam reformatted to the style of the poet ee cummings

2a specific instance of spammings usage of ee spammings: "ee spammings extract a useful dimension from unsolicited communication." example of ee spammings: "please reply / me back i have / something to tell / you (inmportant)" origin of ee spammings: spam + ee cummings see also: spammings

Word circulation status: new ex·ist·angs·ty adjective

1characterized by existential angst, in particular to a small degree

2slightly miffed at the apparent lack of purpose of life and direction of the expanding universe usage of existangsty: "That cosmology video made me existangsty." origin of existangsty: existential + angst

Word circulation status: new fez·day noun

1an occasion, time or day of celebration associated with specific rituals and/or dress, whose origins have been forgotten, with time but usually purposefully, because they harken to a time that was unprosperous, calamitous or embarrassing.

2an unfortunate event whose memory is purposefully perceived as positive to avoid embarrassment or conflict usage of fezday: "They celebrated fezday, like it was a good thing." usage of fezday: "Nobody could remember the origins of fezday, but everyone always had a good time." usage of fezday: "You couldn't tell the celebrants they looked ridiculous at the risk of incuring their wrath, which always seemed close to the surface." usage of fezday: "Let's have a fezday with this." origin of fezday: fez + day. Based on the legendary account of a long-fought battle which ended in a humiliating defeat, made visibly worse by the victor demanding that the losing side wear a fez each year in shame. Many years passed. Over time the losing side's embarrassment and resentment grew. The fez embodied their humiliation and loss, both intolerable. Eventually, the original reason for the fez was struck from historical record. The day was turned into a celebration of independence and identity. The fez became a national symbol and was widely worn.

Word circulation status: new hil·ber·ton·ian noun

1a creature that lives on 3 adjacent orders of the Hilbert curve.

2a creature of one of the 14 classes of Hilbertonians: alien, voyager, crossfit, breaker, spider, sentinel, dasher, creeper, poser, screamer, chopper, veggie, fez and peep. usage of hilbertonian: "I think this Hilbertonian is a creeper." example of hilbertonian: "Classification of Hilbertonians." origin of hilbertonian: from Hilbert curve

Word circulation status: low hive panel noun

1a matrix of hive plots presenting multiple independent visual signatures of a network usage of hive panel: "The hive panels of these two networks helped me see minor differences in structure I would have normally missed." see also: hive plot, ratio hive

Word circulation status: high hive plot noun

1a network visualization method which assigns and positions nodes on linear axes using rules based on structural properties of the network

2periodic parallel axis plot in which the axes are arranged radially, like in a radar plot usage of hive plot: "Hive plots create rational network visualizations that can be easily interpreted and compared." see also: hive panel, ratio hive

Word circulation status: new in·con·ver·si·ble adjective

1typically refering to a statement, something whose converse is illogical or senseless, thereby diluting the substance and information content of the original.

2anything whose converse is senseless, either by definition or logic usage of inconversible: "He concealed the lack of substance in his delivery by long inconversible statements" example of inconversible: "I like to have fun." origin of inconversible: in- (non) and conversible see also: culturally inconversible

Word circulation status: low meta·om·ome noun

1The collection of annotations, such as user comments, literature citations and functional and structural interpretations, of an omome. usage of metaomome: "Many centers lack the computational resources to study the entire omome and, instead, focus on metaomomics — the study of its annotations, a more tractable challenge." example of metaomome: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of metaomome: meta + omeome see also: omeomics, omome

Word circulation status: new mys·ti·fic adjective

1terrific, but for unknown or mysterious reasons

2strangely wonderful usage of mystific: "Waiter, this meal is mystific. Can you give me a hint?" origin of mystific: mysterious + terrific

Word circulation status: new nay·the·ism noun

1a belief system in which it is taken on faith that God does not exist. usage of naytheism: "My position of naytheism is unassailable by the theists because it uses the same modes of reasoning." origin of naytheism: nay + theism see also: naytheist

Word circulation status: new nay·the·ist noun

1a person who takes it on faith that God doesn't exist. usage of naytheist: "As a naytheist, I count on my faith to support my views." origin of naytheist: nay + theism see also: naytheism

Word circulation status: new nes noun

1typically to a yes or no question, a response suggesting that both answers hold equal merit in such balance that deciding is difficult and potentially impossible; distinguished from maybe in that nes does not require the speaker to ever reach a decision, nor communicate their intention to do so. usage of nes: "When John asked me on a date, I said 'nes'." origin of nes: no + yes; counterparts in other languages may exist, such as noui in French (non/oui), jain in German (ja/nein), and niak in Polish (nie/tak) — notice that the order of the words can vary in different languages to create the more appealing combination

Word circulation status: new neu·ro·ter·ror noun

1fear elicited by direct chemical or electrical stimulation of the brain, without an external fearsome stimulus usage of neuroterror: "After the development of aerosolized fear-causing neuromodulators, the courts had a difficult time in determining whether their use was captured by the laws governing the classical definition of terror." see also: neuroterrorism

Word circulation status: new neu·ro·ter·ror·ism noun

1use of neuroterror for coersion or control usage of neuroterrorism: "It was unclear whether last month's incident was an act of neuroterror or simply spontaneous mass panic." see also: neuroterror

Word circulation status: new non·post·er noun

1the guilty's garbage can usage of nonposter: "Looking at the contents of your nonposter, I see that you are not engaged in environmental causes." origin of nonposter: non + composter

Word circulation status: accepted om·ome noun

1The collective set of all omics, such as genomics, proteomics, exomics, metabolomics, etc. example of omome: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of omome: omics + -ome see also: metaomeome, omeomics, omicsophy

Word circulation status: accepted ome·om·ics noun

1synonym for omicsophy example of omeomics: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of omeomics: omics + -sophy see also: metaomeome, omicsophy

Word circulation status: new omic·so·phy noun

1The study of the collection of omics, the broad fields whose name ends in the omics suffix (commonly found in the biological sciences), such as genomics, proteomics, exomics, metabolomics, etc. example of omicsophy: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of omicsophy: omics + -sophy see also: metaomeome, omeomics, omome

Word circulation status: new over noun

1a sleepover, but without sleep, ideally ending in a prekfast. usage of over: "After last night's over, I was exhausted but happy the next day." see also: prekfast

Word circulation status: new pid·dle noun

1liquid unit of measure, equivalent to a pinch

2spontaneous urination from a small, typically obnoxious, dog, amidst excitement

3in general, a small amount of any liquid uncontrollably produced example of piddle: "This Yorkshire pudding recipe calls for a piddle of drippings." origin of piddle: off-label use of piddle

Word circulation status: accepted port knocking noun

1a method in computer security to authenticate a remote host with a server without the use of any open ports usage of port knocking: "My server cannot be detected by a port scan, but I can still login because I use port knocking." origin of port knocking: Krzywinski, M. Port Knocking: Network authentication across closed ports. SysAdmin Magazine (2003) 12:12-17

Word circulation status: new post·pe·ti·zer noun

1a small meal ordered after dessert, consumed during examination and settling of the bill usage of postpetizer: "The desert was delicious but we are still peckish — could you bring us a postpetizer with the bill please?" see also: prepetizer

Word circulation status: new pre·kfast noun

1a light snack, before breakfast, typically prepared and presented by one's sleep partner and consumed in bed usage of prekfast: "She was thoughtful to bring me a prekfast after our over." origin of prekfast: pre + breakfast see also: over

Word circulation status: new pre·nop·sis noun

1a summary, such as of a book, program or event, formed purely on expectation, bias and hope, formulated before the object or event is experienced usage of prenopsis: "Looking at the book's cover in the store, I quickly formulated a prenopsis which proved suprisingly accurate."

Word circulation status: new pre·pe·ti·zer noun

1a small meal, typically delivered quickly, ordered after the arrival, but before reading, of the menu, intended to quench the initial hunger until the arrival of the appetizer usage of prepetizer: "We are starving — could you bring us a prepetizer while we look at the menu?" origin of prepetizer: pre + appetizer similar to: amuse-bouche see also: postpetizer

Word circulation status: new quin·ty adjective

1a person or thing possessing rare or special qualities or traits, thereby potentially embodying the fifth essence usage of quinty: "This dessert is so divine, as to be almost quinty." origin of quinty: diminutive of quintessential, in a more relaxed use

Word circulation status: low ratio hive noun

1a hive plot used to visualize ratio quantities between three or more axes, employing stacked ribbons to show the cumulative distribution of values

2periodic stacked bar plot in which the axes are arranged radially, like in a radar plot usage of ratio hive: "Ratio hives can be used to illustrate differences in composition or structure of various object." see also: hive panel, hive plot

Word circulation status: new spammings noun

1short form of ee spammings

2unsolicited communication reformatted, with poetic license, into a more palatable form see also: ee spammings

Word circulation status: new sus·ci·tate verb

1to raise an individual's life energy so far beyond previous highest level as to give the impression of life for the first time

2to animate, energize, or stimulate an entity to a new level of liveliness.

3(figurative) to breate life into, for the first time usage of suscitate: "Looks like meeting Mary really suscitated John. I've never seen him this alive." origin of suscitate: resuscitate, except without re-, implying that the entity has never lived

news + thoughts

Nested Designs—Assessing Sources of Noise

Mon 29-09-2014

Sources of noise in experiments can be mitigated and assessed by nested designs. This kind of experimental design naturally models replication, which was the topic of last month's column.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Nested designs. (read)

Nested designs are appropriate when we want to use the data derived from experimental subjects to make general statements about populations. In this case, the subjects are random factors in the experiment, in contrast to fixed factors, such as we've seen previously.

In ANOVA analysis, random factors provide information about the amount of noise contributed by each factor. This is different from inferences made about fixed factors, which typically deal with a change in mean. Using the F-test, we can determine whether each layer of replication (e.g. animal, tissue, cell) contributes additional variation to the overall measurement.

Krzywinski, M., Altman, N. & Blainey, P. (2014) Points of Significance: Nested designs Nature Methods 11:977-978.

Background reading

Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.

...more about the Points of Significance column

Replication—Quality over Quantity

Tue 02-09-2014

It's fitting that the column published just before Labor day weekend is all about how to best allocate labor.

Replication is used to decrease the impact of variability from parts of the experiment that contribute noise. For example, we might measure data from more than one mouse to attempt to generalize over all mice.

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

It's important to distinguish technical replicates, which attempt to capture the noise in our measuring apparatus, from biological replicates, which capture biological variation. The former give us no information about biological variation and cannot be used to directly make biological inferences. To do so is to commit pseudoreplication. Technical replicates are useful to reduce the noise so that we have a better chance to detect a biologically meaningful signal.

Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.

Background reading

Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.

...more about the Points of Significance column

Monkeys on a Hilbert Curve—Scientific American Graphic

Tue 19-08-2014

I was commissioned by Scientific American to create an information graphic that showed how our genomes are more similar to those of the chimp and bonobo than to the gorilla.

I had about 5 x 5 inches of print space to work with. For 4 genomes? No problem. Bring out the Hilbert curve!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Our genomes are much more similar to the chimp and bonobo than to the gorilla. And, we're practically still Denisovans. (details)

To accompany the piece, I will be posting to the Scientific American blog about the process of creating the figure. And to emphasize that the genome is not a blueprint!

As part of this project, I created some Hilbert curve art pieces. And while exploring, found thousands of Hilbertonians!

Happy Pi Approximation Day— π, roughly speaking 10,000 times

Wed 13-08-2014

Celebrate Pi Approximation Day (July 22nd) with the art of arm waving. This year I take the first 10,000 most accurate approximations (m/n, m=1..10,000) and look at their accuracy.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Accuracy of the first 10,000 m/n approximations of Pi. (details)

I turned to the spiral again after applying it to stack stacked ring plots of frequency distributions in Pi for the 2014 Pi Day.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Frequency distribution of digits of Pi in groups of 4 up to digit 4,988. (details)