Trance opera—Spente le Stellebe dramatic

# art is science is art

Bioinformatics and Genome Analysis Course. Izmir International Biomedicine and Genome Institute, Izmir, Turkey. May 2–14, 2016

# 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.

circulation level new low medium high accepted

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

pre·grat·ul·ate verb

1offer praise in anticipation of success

2offer contratulations before success is achieved usage of pregratulate: "On my first day of college my parents pregratulated me on my graduation." origin of pregratulate: pre + contratulate see also: prenopsis

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

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."

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

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

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

noun

1short form of ee spammings

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

# Gene Volume Control

Thu 11-06-2015

I was commissioned by Scientific American to create an information graphic based on Figure 9 in the landmark Nature Integrative analysis of 111 reference human epigenomes paper.

The original figure details the relationships between more than 100 sequenced epigenomes and genetic traits, including disease like Crohn's and Alzheimer's. These relationships were shown as a heatmap in which the epigenome-trait cell depicted the P value associated with tissue-specific H3K4me1 epigenetic modification in regions of the genome associated with the trait.

Figure 9 from Integrative analysis of 111 reference human epigenomes (Nature (2015) 518 317–330). (details)

As much as I distrust network diagrams, in this case this was the right way to show the data. The network was meticulously laid out by hand to draw attention to the layered groups of diseases of traits.

Network diagram redesign of the heatmap for a select set of traits. Only relationships with –log P > 3.9 are displayed. Appears on Graphic Science page in June 2015 issue of Scientific American. (details)

This was my second information graphic for the Graphic Science page. Last year, I illustrated the extent of differences in the gene sequence of humans, Denisovans, chimps and gorillas.

# Sampling distributions and the bootstrap

Thu 11-06-2015

The bootstrap is a computational method that simulates new sample from observed data. These simulated samples can be used to determine how estimates from replicate experiments might be distributed and answer questions about precision and bias.

Nature Methods Points of Significance column: Sampling distributions and the bootstrap. (read)

We discuss both parametric and non-parametric bootstrap. In the former, observed data are fit to a model and then new samples are drawn using the model. In the latter, no model assumption is made and simulated samples are drawn with replacement from the observed data.

Kulesa, A., Krzywinski, M., Blainey, P. & Altman, N (2015) Points of Significance: Sampling distributions and the bootstrap Nature Methods 12:477-478.

Krzywinski, M. & Altman, N. (2013) Points of Significance: Importance of being uncertain. Nature Methods 10:809-810.

# Bayesian statistics

Thu 30-04-2015

Building on last month's column about Bayes' Theorem, we introduce Bayesian inference and contrast it to frequentist inference.

Given a hypothesis and a model, the frequentist calculates the probability of different data generated by the model, P(data|model). When this probability to obtain the observed data from the model is small (e.g. alpha = 0.05), the frequentist rejects the hypothesis.

Nature Methods Points of Significance column: Bayesian Statistics. (read)

In contrast, the Bayesian makes direct probability statements about the model by calculating P(model|data). In other words, given the observed data, the probability that the model is correct. With this approach it is possible to relate the probability of different models to identify one that is most compatible with the data.

The Bayesian approach is actually more intuitive. From the frequentist point of view, the probability used to assess the veracity of a hypothesis, P(data|model), commonly referred to as the P value, does not help us determine the probability that the model is correct. In fact, the P value is commonly misinterpreted as the probability that the hypothesis is right. This is the so-called "prosecutor's fallacy", which confuses the two conditional probabilities P(data|model) for P(model|data). It is the latter quantity that is more directly useful and calculated by the Bayesian.

Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of Significance: Bayes' Theorem Nature Methods 12:277-278.

Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of Significance: Bayes' Theorem Nature Methods 12:277-278.

# Bayes' Theorem

Wed 22-04-2015

In our first column on Bayesian statistics, we introduce conditional probabilities and Bayes' theorem

P(B|A) = P(A|B) × P(B) / P(A)

This relationship between conditional probabilities P(B|A) and P(A|B) is central in Bayesian statistics. We illustrate how Bayes' theorem can be used to quickly calculate useful probabilities that are more difficult to conceptualize within a frequentist framework.

Nature Methods Points of Significance column: Bayes' Theorem. (read)

Using Bayes' theorem, we can incorporate our beliefs and prior experience about a system and update it when data are collected.

Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of Significance: Bayes' Theorem Nature Methods 12:277-278.