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

science: fun

In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017

communication + science

Nature Methods: Points of View

Martin Krzywinski @MKrzywinski
Points of View column in Nature Methods. (Points of View)
1 | Krzywinski M 2016 Intuitive design Nat Methods 13:895.
2 | Krzywinski M 2016 Binning high-resolution data Nat Methods 13:463.
3 | Hunnicutt BJ & Krzywinski M 2016 Neural circuit diagrams Nat Methods 13:189.
4 | Hunnicutt BJ & Krzywinski M 2016 Pathways Nat Methods 13:5.
5 | McInerny G & Krzywinski M 2015 Unentangling complex plots Nat Methods 12:591.
6 | Streit M & Gehlenborg N 2015 Temporal Data Nat Methods 12:97.
7 | Lex A & Gehlenborg N 2014 Sets and Intersections Nat Methods 11:778.
8 | Streit M & Gehlenborg N 2014 Bar charts and box plots Nat Methods 11:117.
9 | Krzywinski M & Cairo A 2013 Storytelling Nat Methods 10:687.
10 | Krzywinski M & Savig E 2013 Multidimensional Data Nat Methods 10:595.
11 | Krzywinski M & Wong B 2013 Plotting symbols Nat Methods 10:451.
12 | Krzywinski M 2013 Elements of visual style Nat Methods 10:371.
13 | Krzywinski M 2013 Labels and callouts Nat Methods 10:275.
14 | Krzywinski M 2013 Axes, ticks and grids Nat Methods 10:183.
15 | Wong B 2012 Visualizing biological data Nat Methods 9:1131.
16 | Wong B & Kjaegaard RS 2012 Pencil and paper Nat Methods 9:1037.
17 | Gehlenborg N & Wong B 2012 Power of the plane Nat Methods 9:935.
18 | Gehlenborg N & Wong B 2012 Into the third dimension Nat Methods 9:851.
19 | Gehlenborg N & Wong B 2012 Mapping quantitative data to color Nat Methods 9:769.
20 | Nielsen C & Wong B 2012 Representing genomic structural variation Nat Methods 9:631.
21 | Nielsen C & Wong B 2012 Managing deep data in genome browsers Nat Methods 9:521.
22 | Nielsen C & Wong B 2012 Representing the genome Nat Methods 9:423.
23 | Gehlenborg N & Wong B 2012 Integrating data Nat Methods 9:315.
24 | Gehlenborg N & Wong B 2012 Heat maps Nat Methods 9:213.
25 | Gehlenborg N & Wong B 2012 Networks Nat Methods 9:115.
26 | Shoresh N & Wong B 2012 Data exploration Nat Methods 9:5.
27 | Wong B 2011 The design process Nat Methods 8:987.
28 | Wong B 2011 Salience to relevance Nat Methods 8:889.
29 | Wong B 2011 Layout Nat Methods 8:783.
30 | Wong B 2011 Arrows Nat Methods 8:701.
31 | Wong B 2011 Simplify to clarify Nat Methods 8:611.
32 | Wong B 2011 Avoiding color Nat Methods 8:525.
33 | Wong B 2011 Color blindness Nat Methods 8:441.
34 | Wong B 2011 The overview figure Nat Methods 8:365.
35 | Wong B 2011 Typography Nat Methods 8:277.
36 | Wong B 2011 Points of review (part 2) Nat Methods 8:189.
37 | Wong B 2011 Points of review (part 1) Nat Methods 8:101.
38 | Wong B 2011 Negative space Nat Methods 8:5.
39 | Wong B 2010 Gestalt principles (part 2) Nat Methods 7:941.
40 | Wong B 2010 Gestalt principles (part 1) Nat Methods 7:863.
41 | Wong B 2010 Salience Nat Methods 7:773.
42 | Wong B 2010 Design of data figures Nat Methods 7:665.
43 | Wong B 2010 Color coding Nat Methods 7:573.

news + thoughts

Oryza longistaminata genome cake

Mon 24-09-2018

Data visualization should be informative and, where possible, tasty.

Stefan Reuscher from Bioscience and Biotechnology Center at Nagoya University celebrates a publication with a Circos cake.

The cake shows an overview of a de-novo assembled genome of a wild rice species Oryza longistaminata.

Martin Krzywinski @MKrzywinski
Circos cake celebrating Reuscher et al. 2018 publication of the Oryza longistaminata genome.

Optimal experimental design

Tue 31-07-2018
Customize the experiment for the setting instead of adjusting the setting to fit a classical design.

The presence of constraints in experiments, such as sample size restrictions, awkward blocking or disallowed treatment combinations may make using classical designs very difficult or impossible.

Optimal design is a powerful, general purpose alternative for high quality, statistically grounded designs under nonstandard conditions.

Martin Krzywinski @MKrzywinski
Nature Methods Points of Significance column: Optimal experimental design. (read)

We discuss two types of optimal designs (D-optimal and I-optimal) and show how it can be applied to a scenario with sample size and blocking constraints.

Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design Nature Methods 15:599–600.

Background reading

Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.

Krzywinski, M. & Altman, N. (2014) Points of significance: Analysis of variance (ANOVA) and blocking. Nature Methods 11:699–700.

Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments. Nature Methods 11:597–598.

The Whole Earth Cataloguer

Mon 30-07-2018
All the living things.

An illustration of the Tree of Life, showing some of the key branches.

The tree is drawn as a DNA double helix, with bases colored to encode ribosomal RNA genes from various organisms on the tree.

Martin Krzywinski @MKrzywinski
The circle of life. (read, zoom)

All living things on earth descended from a single organism called LUCA (last universal common ancestor) and inherited LUCA’s genetic code for basic biological functions, such as translating DNA and creating proteins. Constant genetic mutations shuffled and altered this inheritance and added new genetic material—a process that created the diversity of life we see today. The “tree of life” organizes all organisms based on the extent of shuffling and alteration between them. The full tree has millions of branches and every living organism has its own place at one of the leaves in the tree. The simplified tree shown here depicts all three kingdoms of life: bacteria, archaebacteria and eukaryota. For some organisms a grey bar shows when they first appeared in the tree in millions of years (Ma). The double helix winding around the tree encodes highly conserved ribosomal RNA genes from various organisms.

Johnson, H.L. (2018) The Whole Earth Cataloguer, Sactown, Jun/Jul, p. 89

Why we can't give up this odd way of typing

Mon 30-07-2018
All fingers report to home row.

An article about keyboard layouts and the history and persistence of QWERTY.

My Carpalx keyboard optimization software is mentioned along with my World's Most Difficult Layout: TNWMLC. True typing hell.

Martin Krzywinski @MKrzywinski
TNWMLC requires seriously flexible digits. It’s 87% more difficult than using a standard Qwerty keyboard, according to Martin Krzywinski, who created it (Credit: Ben Nelms). (read)

McDonald, T. (2018) Why we can't give up this odd way of typing, BBC, 25 May 2018.

Molecular Case Studies Cover

Fri 06-07-2018

The theme of the April issue of Molecular Case Studies is precision oncogenomics. We have three papers in the issue based on work done in our Personalized Oncogenomics Program (POG).

The covers of Molecular Case Studies typically show microscopy images, with some shown in a more abstract fashion. There's also the occasional Circos plot.

I've previously taken a more fine-art approach to cover design, such for those of Nature, Genome Research and Trends in Genetics. I've used microscopy images to create a cover for PNAS—the one that made biology look like astrophysics—and thought that this is kind of material I'd start with for the MCS cover.

Martin Krzywinski @MKrzywinski
Cover design for Apr 2018 issue of Molecular Case Studies. (details)