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Thoughts rearrange, familiar now strange.Holly Golightly & The Greenhornes break flowersmore quotes

noise: worthwhile


Scientific graphical abstracts — design guidelines


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

Music for the Moon: Flunk's 'Down Here / Moon Above'

Sat 29-05-2021

The Sanctuary Project is a Lunar vault of science and art. It includes two fully sequenced human genomes, sequenced and assembled by us at Canada's Michael Smith Genome Sciences Centre.

The first disc includes a song composed by Flunk for the (eventual) trip to the Moon.

But how do you send sound to space? I describe the inspiration, process and art behind the work.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The song 'Down Here / Moon Above' from Flunk's new album History of Everything Ever is our song for space. It appears on the Sanctuary genome discs, which aim to send two fully sequenced human genomes to the Moon. (more)

Browse the genome discs.

Happy 2021 `\pi` Day—
A forest of digits

Sun 14-03-2021

Celebrate `\pi` Day (March 14th) and finally see the digits through the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 26th tree in the digit forest of `\pi`. Why is there a flower on the ground?. (details)

This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first 46 digits of `\pi` in 8 trees. There are so many more. (details)

And things can get crazy in the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A forest of the digits of '\pi`, by ecosystem. (details)

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, 2018 `\pi` Day and 2019 `\pi` Day.

Testing for rare conditions

Sun 30-05-2021

All that glitters is not gold. —W. Shakespeare

The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.

We discuss the positive predictive value (PPV) and how practices such as screen can increase it.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Testing for rare conditions. (read)

Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18:224–225.

Standardization fallacy

Tue 09-02-2021

We demand rigidly defined areas of doubt and uncertainty! —D. Adams

A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.

Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.

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

Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.

Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.

Graphical Abstract Design Guidelines

Fri 13-11-2020

Clear, concise, legible and compelling.

Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.