Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
And whatever I do will become forever what I've done.Wislawa Szymborskadon't rehearsemore quotes

words: fun


Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca
2020 `\pi` day art and the piku


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

The Outbreak Poems

Sat 04-04-2020

I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.

Patience but
know
where to put it.
Favourite 
looks
words tastes phrases
ex
foreign origins.
Melody
same
feelings different.
Desire
life
remote control.
Sun rays burn
off
night dust into
day.
Sanitize
in
perfection now.
Door closes
next
next door closes
next
nothing is left open.
One of the
pair
is from the other.
Eyes look at
eyes
and see themselves.
Look back and
pass
destinations.

Read the poems and learn what a piku is.

Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses

Tue 17-03-2020

A poster full of epidemiological worry and statistics. Now updated with the genome of SARS-CoV-2 and COVID-19 case statistics as of 3 March 2020.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

Bacterial and viral genomes of various diseases are drawn as paths with color encoding local GC content and curvature encoding local repeat content. Position of the genome encodes prevalence and mortality rate.

The deadly genomes collection has been updated with a posters of the genomes of SARS-CoV-2, the novel coronavirus that causes COVID-19.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first SARS-CoV-2 genome (MT019529) to be sequenced appears first on the poster.

Using Circos in Galaxy Australia Workshop

Wed 04-03-2020

A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Using Circos in Galaxy Australia workshop. (zoom)

Download workshop slides.

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).

Essence of Data Visualization in Bioinformatics Webinar

Thu 20-02-2020

My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Essence of Data Visualization in Bioinformatics webinar. (zoom)

Download webinar slides.

Markov models — training and evaluation of hidden Markov models

Thu 20-02-2020

With one eye you are looking at the outside world, while with the other you are looking within yourself.
—Amedeo Modigliani

Following up with our Markov Chain column and Hidden Markov model column, this month we look at how Markov models are trained using the example of biased coin.

We introduce the concepts of forward and backward probabilities and explicitly show how they are calculated in the training process using the Baum-Welch algorithm. We also discuss the value of ensemble models and the use of pseudocounts for cases where rare observations are expected but not necessarily seen.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Markov models — training and evaluation of hidden Markov models. (read)

Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Markov models — training and evaluation of hidden Markov models. Nature Methods 17:121–122.

Background reading

Altman, N. & Krzywinski, M. (2019) Points of significance: Hidden Markov models. Nature Methods 16:795–796.

Altman, N. & Krzywinski, M. (2019) Points of significance: Markov Chains. Nature Methods 16:663–664.

Genome Sciences Center 20th Anniversary Clothing, Music, Drinks and Art

Tue 28-01-2020

Science. Timeliness. Respect.

Read about the design of the clothing, music, drinks and art for the Genome Sciences Center 20th Anniversary Celebration, held on 15 November 2019.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Luke and Mayia wearing limited edition volunteer t-shirts. The pattern reproduces the human genome with chromosomes as spirals. (zoom)

As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Precisely engineered frame mounts of flow cells used to sequence genomes in our laboratory. (zoom)

Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The plaque at the back of one of the framed Illumina flow cell. This one has sequence from a patient's lymph node diagnosed with Burkitt's lymphoma. (zoom)