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
Poetry is just the evidence of life. If your life is burning well, poetry is just the ashLeonard Cohenburn somethingmore quotes

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Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca

2020 `\pi` day art and the piku


BCGSC.CA 10TH ANNIV AdrianALLY JianghongAN RuthAPPANAH LukeARMSTRONG JenniferASANO MehranATAEE TimothyAU-YEUNG JosieAUDET HeatherAXAM LanceBAILEY MirunaBALA AdrianaBANUELOS LorenaBARCLAY MishaBILENKY InancBIROL IanBOSDET KarlaBRETHERICK AngelaBROOKS-WILSON MabelBROWN-JOHN RichardBRUSKIEWICH YaronBUTTERFIELD RebeccaCARLSEN MauroCASTELLARIN TimotheeCEZARD SusannaCHAN SimonCHAN JustinCHAN ClintonCHAN SteveCHAND Chi-DanCHANG AnitaCHARTERS DeborahCHEN GraceCHENG DeanCHENG DorothyCHEUNG RodneyCHIN SuganthiCHITTARANJAN ReadmanCHIU StephanieCHO GinaCHOE RobertCHRISP AndyCHU EricCHUAH ElizabethCHUN StellaCHUN LouiseCLARKE AmandaCLARKE RobinCOOPE RichardCORBETT MonicaCORNEAN AdrianCORTES LuluCRISOSTOMO KattyCRUZ CletusD'SOUZA AllenDELANEY AthenaDENG MerindaDENG LindsayDEVORKIN NoreenDHALLA RodDOCKING LisaDREOLINI AdrienneDROBNIES MadaleneEARP AmyENGLISH NoushinFARNOUD AnthonyFEJES CynthiaFERGUSON MatthewFIELD StephaneFLIBOTTE DanFORNIKA DougFREEMAN FrancisFRENO MarilynGILLESPIE BeckyGILLESPIE NatalieGLAVAS SharonGORSKI RodrigoGOYA MalachiGRIFFITH ObiGRIFFITH RanGUIN ImanHAJIRASOULIHA JuliusHALASCHEK-WIENER AdamHALL AdrienneHANNIGAN JenniferHARDIE RubayetHASAN AnHE SeanHENDERSON UljanaHESSE MartinHIRST CarrieHIRST RobertHOLT DanielHORSPOOL ClaireHOU JayneHUNTER TakaakiICHU ShaunJACKMAN CarrieJANG RozminJANOO-GILANI KelseyJEFFERSON JupiterJIANG ChaoyangJIN LindseyJOHNSON JoanneJOHNSON StevenJONES BaljitKAMOH MiraKARIA KatayoonKASAIAN UsmanKHAN JieunKIM HeatherKIRK MartinKRZYWINSKI LetticiaKWONG DarwinLAHUE AnthonyLE StephenLEACH DarleneLEE Hyun-WuLEE AmyLEUNG DidiLEUNG YvonneLI IreneLI SaLI NancyLIAO YuSiLIU KevinMA DianaMAH NawarMALHIS MarcoMARRA CoreyMATSUO RinaMAWJI NasrinMAWJI LorraineMAY MichaelMAYO HelenMCDONALD StephanieMCINNIS HeatherMCMURTRIE Carri-LynMEAD MariaMENDEZ-LAGO SimonHaileMERHU DianeMILLER MichelleMOKSA RichardMOORE AnnieMORADIAN RyanMORIN GreggMORIN OlenaMOROZOVA AndyMUNGALL KarenMUNGALL SarahMUNRO JillMWENIFUMBO Jae-KyungMYUNG RichardNEWSOME JoanNG CydneyNIELSEN KarenNOVIK DianaPALMQUIST PawanPANDOH JohnsonPANG IrenePELOSO LinhPHAN ReneePICHE Anna-LiisaPRABHU TrevorPUGH JennyQIAN LisaRAEBURN RitaRAHARJO MaziarRAHMANI JianhuaREN GordonROBERTSON RobynROSCOE RouzbehROSHANRAVAN SharonRUSCHKOWSKI DanneSA MarianneSADAR MurwanSALAME RolandSANTOS JacquieSCHEIN JohannaSCHUETZ TesaSEVERSON ArashSHAFIEI HeesunSHIN SanjitSINGH RanjitSINGH JaredSLOBODAN DuaneSMAILUS JillianSMITH RichardSOBEL SoranaMORRISSY GregSTAZYK DominikSTOLL CeceliaSURAGH Wing-KaSZE IsabellaTAI AngelaTAM BonnyTAM TeresaTAM SamuelTAN MichelleTANG GregTAYLOR KevinTEAGUE NinaTHIESSEN KenTHORNE TinaTHORNE AncaTOMESCU EvaTRINH ArmelleTROUSSARD MirandaTSAI KaneTSE RichardVARHOL SusanWAGNER GangWANG JeanWANG ReneWARREN DenilWICKRAMA MiriamWILLIAMS GaryWILSON TinaWONG JohnWONG KenWRIGHT JacksonWU NatasjaWYE AlexanderYAKOVENKO GeorgeYANG KevinYANG RunyingYANG DenizYORUKOGLU ThomasZENG XuekuiZHANG YongjunZHAO MiZHOU 261109mk

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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.

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)

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