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And whatever I do will become forever what I've done.Wislawa Szymborskadon't rehearsemore quotes

EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.


language + fiction

Dark Matter of the English Language—the unwords

Words are easy, like the wind;
Faithful friends are hard to find.
—William Shakespeare

undrugs

These are names generated from a list of 24,454 drug names.

—4—
abur
baca
cict
dars
ebar
flud
gada
ibii
jefs
kafi
lall
mali
naax
opmo
pali
rano
selt
tawe
ucci
vacp
wens
xafa
—5—
abans
babax
calen
dafur
ebane
facol
gacil
iacos
jadan
kadex
labet
makan
nacil
oxags
paflu
quare
rabax
secte
tacin
uccar
vabex
wanda
xaaix
yslel
zasum
—6—
abaloe
babuck
calcyn
dacter
ebalen
facgol
gaadop
hincal
ibinum
jedbit
kabone
laaful
magars
nabrem
oxatho
pactug
quafen
rabine
secteg
tabora
ucicin
vabaib
wanosa
xabert
yrsect
zalace
—7—
abaacyd
baadate
calchox
dactsal
ebancel
facacon
gabaxin
iakinic
jedinee
kabcale
labigen
magunal
nacamin
oxaciol
pacterh
qausans
raamene
salivac
tacicyn
uccosil
vababen
wanptax
xabiban
zinomem
—8—
abadixal
bababate
cainecin
dactagul
ebalicin
fabrolil
gablexal
hikazium
ialmloxe
jedlotin
kabomide
laberome
majcogen
nabcidel
otrustin
pactecin
quactowa
rabimist
sebumest
tacillep
ucbucine
vabafora
wedamate
xabatyce
ylyutate
zalcperm
—9—
abadarone
babaridol
calbimyne
dacriness
ebacycate
facantase
gabrigine
hyticelin
iamasdist
jefarinon
kadolilol
labromine
majyctied
naccyfius
oxamprens
pactitone
quafedate
rabinozil
sdavotrin
taaknolse
ucchidemt
vababular
wancromin
xabancald
zenezumin
—10—
abisarprin
baborastin
calbenzode
dabotarone
ebaldentan
fabridibil
gabrizelin
iarareblol
jedcinimib
kabletesin
laalfemate
malbevoled
nacatemine
oximucaine
pacteticin
quaminevra
rabibretan
sectexasin
tacraldran
uclocollan
vabacloxan
wemgmittex
xacirdosal
zolkopacul

—11—
abithyltine
babaszolate
calbicyrone
dactavirine
ebarmolofal
fabatrastin
gabacpromat
hentrocaine
iamicaptide
jenxesamlan
kabentiquin
lacinylfare
mahygsotrou
naceguldine
omimefcaile
pactricofyl
quadiradine
rabionimone
seclonedine
tacoilcuria
udobycerino
vabfazupine
wantdabinal
xabotrazole
—12—
abithyzyrose
babsserizide
calbicyldine
dadtylditrol
ebadregepsil
fabolapeptin
gabridiamide
iazolamicide
kalachoglate
labrossasone
malbitoprime
nabpriletone
oxilophenape
palbinolenal
quaraleniont
rabinilamide
sectallolaen
taclocarbral
udobentitone
vacisastamin
wenosanterix
xalmuziquine
ysictanamine
—13—
abrvanrinabin
baadilocyctos
calchantrolec
danphorpophin
ebapyfenazine
fabocrocalise
gadizocilcein
ibormormidine
kacumycansint
laciveliamide
maldimiszidis
nacciricillin
oxiprimetmine
pacthinatesul
quadrintroram
rachometremin
seginuskatate
tabconcaneute
udloxexeneate
vabagraineone
xencoonyprone
—14—
abisulgoradine
babelozadrocin
calbonamperine
daploseinticyl
ecloincolthose
factismaztosta
gacroscelazine
ibectilycravon
jedipronobreke
kalsvinitherat
laditamastinic
malmistolamine
narbadoloquine
palbiflapritar
quaquinonostiq
raccilchocalte
seliglhytririd
talinohydracin
ulophynonamide
valisulfatrium
xastumyphideve
—15—
abrinechedrophe
badoriprozamine
calbidomycinnix
dehydrocyrfoide
ebavhmacetamide
fentafanfenthol
gamasoponeferox
henthichloreder
icophortitinase
kallucinroylmax
lantimethranone
maldoglotranone
natiphretamicid
panssormvestisa
quaminpropyrate
rabidratethotel
secpherinesetol
talphomectivine
ulnimachcrabine
vanaibevyllsten
xenozeroracitic

—16—
abistartolexbant
bacthifulvastols
calphamycinsapol
deltrocalfromide
eclacateproficel
fentencarbetosin
galicalcyacpiran
halitsiongoneoko
icarvisonediranc
kalkundyprimicin
lamorfertellucid
malivitaplothium
narbegeneictosol
panstantrinebune
quardinecaaptine
rafinesytkutoril
selbongathiazode
talinatromethine
ulopachlipralone
vacliclehanazole
winnasdinuelilus
—17—
abitionesanserxan
babetulsosportrin
caldinephhenosone
dehydichotagelgil
ellocirlicmedhyne
fentaguufsanodine
gaditoxypuniticin
icgronumtatogycid
karfinebenthichin
lapasinidobeptone
malcidochlirocate
narbamymineterone
paflerfanophyllea
quateylmatithives
ralinkoumfapheton
senicttynetemersh
taliocarfonitrate
ulvutomethonguine
valumindesuanvart
—18—
acamisumsindewobun
bacintypilacingeen
centacagcorteamide
demotetromotoxecin
elirfelateciclazol
fenparmecrilhiculc
galonimaclecrilast
imanacetofyrtazole
kenithadebatreciga
ladisylprabumamide
mantheralbistrocin
natroneshinetrofol
oxirinechloraplite
panprapethinteride
quinhyllazoxamines
rafentrolpaccelgor
seltastrelsortonem
talichloreytrimino
valycrastolefloryl
xorethroxydipantsh
—19—
acedetkesurlumoteen
balinegademetsapine
calfitholeminofuryl
dapsareminephafline
ebalbolnotetrecolen
fadunaziquinonhazol
gankyomicorcatuthri
ickansuecubicanacik
kanizinoessodeinesa
laltostenoxitrogall
mantrinonysrogarone
narbesemanthlacoate
otocrooneserbaaprod
parbimineaprokaprin
ractadadotancmudein
sentapcixynethionen
talicuroidslutorate
ventitalportigastis
xarbethymylazoquine

Below are some families of drugs.

–nines

—6—
binine
kenine
lenine
penine
ranine
sonine
—7—
alinine
bernine
emunine
imanine
leonine
maonine
pernine
sernine
trenine
valnine
—8—
actinine
banenine
dixinine
embonine
ginonine
idranine
letonine
medunine
nemonine
perinine
raconine
semenine
teginine
vanonine
—9—
adefinine
bandonine
cicronine
dapganine
ebapinine
gentanine
imidinine
lentenine
marbinine
nestinine
parbonine
rachenine
senrinine
teldanine
varpenine
—10—
abustanine
balosanine
centrenine
detavenine
ebastinine
fenoranine
galulonine
icosrinine
ledorinine
mantranine
navalanine
pentronine
quartinine
ramoconine
selutinine
talotanine
valipenine
xinezinine
—11—
acinofenine
banefgonine
centazonine
demotrinine
emalitinine
fafvuranine
ganficonine
imatitonine
ladrogenine
maluphenine
naxibrinine
parbidinine
quinitonine
recrotinine
serbabinine
telletinine
urisominine
ventipanine
—12—
aconophanine
baldrifinine
centridonine
dibhustanine
emipormunine
gentrofynine
imbomylinine
lenocenonine
meatastanine
nefectaonine
pelquinonine
rapatalonine
temoceginine
vassingenine

–caines

—8—
bancaine
emucaine
imocaine
silcaine
tescaine
—9—
aclicaine
bericaine
cimocaine
ecuocaine
ferecaine
gapmcaine
icnocaine
kenocaine
letocaine
mexocaine
nexacaine
pallcaine
redocaine
sectcaine
tarocaine
—10—
alidacaine
bandtcaine
centocaine
denticaine
emilocaine
fentocaine
gampacaine
impmacaine
kentecaine
ladricaine
metracaine
netrocaine
oximucaine
pantocaine
rerpacaine
sertacaine
termacaine
vavfycaine
—11—
adronicaine
bentrocaine
galimycaine
hentrocaine
imbonacaine
kallascaine
lezinocaine
methylcaine
nibriscaine
penetacaine
quasalcaine
rerapycaine
sentrocaine
telinecaine
—12—
alfagrecaine
bistipacaine
centomicaine
estarcicaine
galmoxocaine
imodicecaine
mantolacaine
northrocaine
penanfocaine
restolocaine
sulfolucaine
tenthricaine
—13—
antiethycaine
entrodrocaine
fentionicaine
intiminocaine
norfydrocaine
penittelcaine
relonolacaine
testotrocaine

–cillins

—8—
docillin
incillin
—9—
barcillin
icocillin
malcillin
vescillin
—10—
alfacillin
bimocillin
dicocillin
esvocillin
impocillin
kalocillin
lamocillin
muticillin
pericillin
senicillin
timocillin
vanacillin
—11—
aminocillin
baloncillin
ekitocillin
fenticillin
iminecillin
kipracillin
ledrocillin
mectocillin
pellacillin
quinecillin
serbicillin
termacillin
vertocillin
—12—
amtomicillin
barilucillin
gentiocillin
imoprocillin
letinocillin
metimucillin
nephricillin
pentracillin
renucicillin
teroxacillin
—13—
badergicillin
centobicillin
eximabicillin
laglyrocillin
mecurpicillin
nacciricillin
pentoumcillin
theroxocillin

–ycins

—8—
alomycin
barbycin
dermycin
egamycin
imamycin
leezycin
morxycin
pertycin
sincycin
teprycin
udomycin
—9—
aclomycin
balomycin
camisycin
deximycin
emdimycin
fovemycin
gantrycin
icoaxycin
kaxamycin
lenomycin
metamycin
nemulycin
paramycin
ratomycin
sexocycin
tefomycin
vanimycin
—10—
alifomycin
baclazycin
centohycin
dibromycin
elaromycin
fentimycin
gentomycin
imalomycin
kalmomycin
ledromycin
mantomycin
natromycin
pantobycin
ranafhycin
selkomycin
tectamycin
valmomycin
—11—
aclefomycin
balacomycin
centramycin
deletomycin
emathamycin
fulpremycin
gamutamycin
imminemycin
lenfrimycin
mepaxidycin
nerolamycin
pangetbycin
quinaclycin
remazonycin
seremylycin
tamopomycin
valoxamycin
—12—
alfunnemycin
bamneramycin
diclodomycin
ercrolomycin
ferlonomycin
ganostamycin
imcairimycin
letophomycin
marbinomycin
narbetamycin
pelbetamycin
rexopromycin
serbitomycin
tafofrimycin
vatithamycin
—13—
alfaginamycin
balfolromycin
dichloromycin
emimestomycin
ferrinoplycin
imcitadolycin
lestaclimycin
mantogremycin
norphenimycin
pantrolimycin
siclocolmycin
telivedicycin

–virs

—6—
alovir
banvir
emovir
kenvir
penvir
—7—
adrovir
balevir
dinovir
genevir
iclyvir
linovir
medavir
nefovir
penevir
quarvir
ramivir
temovir
valivir
—8—
alflovir
balmivir
cenmavir
dermevir
ecthavir
fermovir
indravir
kinnuvir
lectovir
nefluvir
oxonivir
pentivir
restevir
serbevir
tentavir
ventivir
xydrivir
—9—
allolovir
balynevir
embitevir
ferolivir
gadilovir
iblosivir
kenolavir
laxitavir
nacinivir
paritovir
renonivir
sergofvir
tegabivir
vartrovir
—10—
alopolovir
baflenovir
diclofavir
endatlivir
ixryasevir
northrivir
paloglevir
restomavir
sertumavir
teneflovir
—11—
alilathevir
borotehivir
embroprovir
intralmovir
lixacycevir
monpretovir
perdabrevir
synonshavir
terglumavir
—12—
antimatlavir
pentimurovir
sulfavinavir
terinobravir
vavinactyvir

VIEW ALL

news + thoughts

`k` index: a weightlighting and Crossfit performance measure

Wed 07-06-2017

Similar to the `h` index in publishing, the `k` index is a measure of fitness performance.

To achieve a `k` index for a movement you must perform `k` unbroken reps at `k`% 1RM.

The expected value for the `k` index is probably somewhere in the range of `k = 26` to `k=35`, with higher values progressively more difficult to achieve.

In my `k` index introduction article I provide detailed explanation, rep scheme table and WOD example.

Dark Matter of the English Language—the unwords

Wed 07-06-2017

I've applied the char-rnn recurrent neural network to generate new words, names of drugs and countries.

The effect is intriguing and facetious—yes, those are real words.

But these are not: necronology, abobionalism, gabdologist, and nonerify.

These places only exist in the mind: Conchar and Pobacia, Hzuuland, New Kain, Rabibus and Megee Islands, Sentip and Sitina, Sinistan and Urzenia.

And these are the imaginary afflictions of the imagination: ictophobia, myconomascophobia, and talmatomania.

And these, of the body: ophalosis, icabulosis, mediatopathy and bellotalgia.

Want to name your baby? Or someone else's baby? Try Ginavietta Xilly Anganelel or Ferandulde Hommanloco Kictortick.

When taking new therapeutics, never mix salivac and labromine. And don't forget that abadarone is best taken on an empty stomach.

And nothing increases the chance of getting that grant funded than proposing the study of a new –ome! We really need someone to looking into the femome and manome.

Dark Matter of the Genome—the nullomers

Wed 31-05-2017

An exploration of things that are missing in the human genome. The nullomers.

Julia Herold, Stefan Kurtz and Robert Giegerich. Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 9:167

Clustering

Wed 31-05-2017
Clustering finds patterns in data—whether they are there or not.

We've already seen how data can be grouped into classes in our series on classifiers. In this column, we look at how data can be grouped by similarity in an unsupervised way.

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

We look at two common clustering approaches: `k`-means and hierarchical clustering. All clustering methods share the same approach: they first calculate similarity and then use it to group objects into clusters. The details of the methods, and outputs, vary widely.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Clustering. Nature Methods 14:545–546.

Background reading

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Logistic regression. Nature Methods 13:541-542.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Classifier evaluation. Nature Methods 13:603-604.

...more about the Points of Significance column

What's wrong with pie charts?

Thu 25-05-2017

In this redesign of a pie chart figure from a Nature Medicine article [1], I look at how to organize and present a large number of categories.

I first discuss some of the benefits of a pie chart—there are few and specific—and its shortcomings—there are few but fundamental.

I then walk through the redesign process by showing how the tumor categories can be shown more clearly if they are first aggregated into a small number groups.

(bottom left) Figure 2b from Zehir et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. (2017) Nature Medicine doi:10.1038/nm.4333

Tabular Data

Tue 11-04-2017
Tabulating the number of objects in categories of interest dates back to the earliest records of commerce and population censuses.

After 30 columns, this is our first one without a single figure. Sometimes a table is all you need.

In this column, we discuss nominal categorical data, in which data points are assigned to categories in which there is no implied order. We introduce one-way and two-way tables and the `\chi^2` and Fisher's exact tests.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Tabular data. Nature Methods 14:329–330.

...more about the Points of Significance column