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
Trance opera—Spente le Stellebe dramaticmore quotes

noise: deep


The Outbreak Poems — artistic emissions in a pandemic


science + music
Hear the Gene machines: the music of a modern genomics laboratory. Music by Segue. Album release by ADSR Collective. Video by Sam King.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Segue Gene Machines - retro desktops.



Gene Machines by Segue (Jordan Sauer) - A collaboration with Canada's Michael Smith Genome Sciences Centre / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
In commemoration of the 20th anniversary of Canada's Michael Smith Genome Sciences Centre, Segue was commissioned to create an original composition based on audio recordings from the GSC's laboratory equipment, robots and computers—to make 'music' from the noise they produce. (Vinyl crowdfunding, Digital preorder, Album preview)

The cover of the album is based on my information graphic of gene expression designed for Scientific American Graphic Science.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The cover of Gene Machines shows expression profiles of a set of genes that cycle their activity throughout the day based on circadian rhythms.
An assembly of shifting soundscapes, textures and rhythmic loops produced by laboratory machines.
a bb 3000 micro centrifuge automation
b server room mini centrifuge thermal cycler
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The album features the sounds from around our laboratory including the Beckman Biomeck 3000 and Hamilton Starlet liquid handling robots, thermocyclers, centrifuges and our server room.

bb 3000

Curious machines explore the mysteries of a tumor cell. If you listen carefully, you can hear them hum to themselves and each other. It’s their way of talking.

micro centrifuge

A compact and low profile centrifuge with whisper-quiet operation and extremely fast acceleration and braking. The motorized latch secures the lid and rotary knobs allow fast parameter selection.

Relative centrifugal field (RCF) is the centrifugal force generated by a rotor of radius `R` (cm) spinning at a speed `S` (rpm). It is expressed in units of the Earth’s acceleration due to gravity, `g = 9.8 \, \text{m} / \text{s}^2` and given by `\text{RCF} = 1.118\times10^{–5}RS^2`

MAXIMUM RCF

16,000 g

CAPACITY

24 × 1.5/2.0 mL tubes

SPEED

800–13,200 rpm

automation

Robots automate liquid handling with interchangeable single or eight channel pipettes that can accommodate various tips. They are used to normalize samples, set up chemical reactions, or SPRI bead-clean samples prior to loading sequencers.

CAPACITY

30 tracks

WASH TIME

45 sec/cycle

TIP VOLUME

10, 50, 300, 1,000 μL

PRECISION

1%, 0.75%, 0.75%, 0.75%

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The machinery of side A in detail.

server room

Computational pipelines and databases process more than 100 terabases of sequence per month.

BASES SEQUENCED

2,825,069,728,668,255

CORES

30,000

Dell Intel E5

HPE E7 2.5Tb high-memory servers

STORAGE

24 PB

EMC Isilon X410

EMC A2000

NetApp 9000

DDN GS12K + GridScalar

NETWORK

40 Gbps

Brocade MLX Layer 2

Ruckus ICX Layer3

mini centrifuge

This compact centrifuge provide a quick method to spin down samples from the walls and caps of microcentrifuge tubes.

MAXIMUM RCF

2,000 g

CAPACITY

6 × 1.5/2.0 mL tubes

SPEED

6,000 rpm

thermal cycler

The thermal cycler was instrumental to the Human Genome Project.It is used to amplify DNA libraries prior to loading onto DNA sequencers.

RANGE

–5°C – 105°C

ACCURACY

±0.3°C

DENATURE

5' 95°C

CUT & KILL

60' 37°C

5' 70°C

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The machinery of side B in detail.

VIEW ALL

news + thoughts

"This data might give you a migrane"

Tue 06-10-2020

An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A poster of high BMI and obesity prevalence for 185 countries.

He said, he said — a word analysis of the 2020 Presidential Debates

Thu 01-10-2020

Building on the method I used to analyze the 2008, 2012 and 2016 U.S. Presidential and Vice Presidential debates, I explore word usagein the 2020 Debates between Donald Trump and Joe Biden.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Analysis of word usage by parts of speech for Trump and Biden reveals insight into each candidate.

Points of Significance celebrates 50th column

Mon 24-08-2020

We are celebrating the publication of our 50th column!

To all our coauthors — thank you and see you in the next column!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance: Celebrating 50 columns of clear explanations of statistics. (read)

Uncertainty and the management of epidemics

Mon 24-08-2020

When modelling epidemics, some uncertainties matter more than others.

Public health policy is always hampered by uncertainty. During a novel outbreak, nearly everything will be uncertain: the mode of transmission, the duration and population variability of latency, infection and protective immunity and, critically, whether the outbreak will fade out or turn into a major epidemic.

The uncertainty may be structural (which model?), parametric (what is `R_0`?), and/or operational (how well do masks work?).

This month, we continue our exploration of epidemiological models and look at how uncertainty affects forecasts of disease dynamics and optimization of intervention strategies.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (read)

We show how the impact of the uncertainty on any choice in strategy can be expressed using the Expected Value of Perfect Information (EVPI), which is the potential improvement in outcomes that could be obtained if the uncertainty is resolved before making a decision on the intervention strategy. In other words, by how much could we potentially increase effectiveness of our choice (e.g. lowering total disease burden) if we knew which model best reflects reality?

This column has an interactive supplemental component (download code) that allows you to explore the impact of uncertainty in `R_0` and immunity duration on timing and size of epidemic waves and the total burden of the outbreak and calculate EVPI for various outbreak models and scenarios.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Uncertainty and the management of epidemics. Nature Methods 17.

Background reading

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.

Cover of Nature Genetics August 2020

Mon 03-08-2020

Our design on the cover of Nature Genetics's August 2020 issue is “Dichotomy of Chromatin in Color” . Thanks to Dr. Andy Mungall for suggesting this terrific title.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Dichotomy of Chromatin in Color. Nature Genetics, August 2020 issue. (read more)

The cover design accompanies our report in the issue Gagliardi, A., Porter, V.L., Zong, Z. et al. (2020) Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes. Nature Genetics 52:800–810.