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Love itself became the object of her love.Jonathan Safran Foercount sadnessesmore quotes

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.

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news + thoughts

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.

Poster Design Guidelines

Wed 15-07-2020

Clear, concise, legible and compelling.

The PDF template is a poster about making posters. It provides design, typography and data visualiation tips with minimum fuss. Follow its advice until you have developed enough design sobriety and experience to know when to go your own way.

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

The SEIRS model for infectious disease dynamics

Thu 18-06-2020

Realistic models of epidemics account for latency, loss of immunity, births and deaths.

We continue with our discussion about epidemic models and show how births, deaths and loss of immunity can create epidemic waves—a periodic fluctuation in the fraction of population that is infected.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: The SEIRS model for infectious disease dynamics. (read)

This column has an interactive supplemental component (download code) that allows you to explore epidemic waves and introduces the idea of the phase plane, a compact way to understand the evolution of an epidemic over its entire course.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: The SEIRS model for infectious disease dynamics. (Interactive supplemental materials)

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.

Background reading

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

Gene Machines

Fri 05-06-2020

Shifting soundscapes, textures and rhythmic loops produced by laboratory machines.

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Gene Machines by Segue. Now available on vinyl.

Virus Mutations Reveal How COVID-19 Really Spread

Mon 01-06-2020

Genetic sequences of the coronavirus tell story of when the virus arrived in each country and where it came from.

Our graphic in Scientific American's Graphic Science section in the June 2020 issue shows a phylogenetic tree based on a snapshot of the data model from Nextstrain as of 31 March 2020.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Virus Mutations Reveal How COVID-19 Really Spread. Text by Mark Fischetti (Senior Editor), art direction by Jen Christiansen (Senior Graphics Editor), source: Nextstrain (enabled by data from GISAID).