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statistics: beautiful



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


statistics + data

Nature Methods: Points of Significance

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Points of Significance column in Nature Methods. (Launch of Points of Significance)

Access all columns for free at Statistics for Biologists Nature Collection.

A Statistics Primer and Best Practices

The Points of Significance column was launched in September 2013 as an educational resource to authors and to provide practical suggestions about best practices in statistical analysis and reporting.

This month we launch a new column "Points of Significance" devoted to statistics, a topic of profound importance for biological research, but one that often doesn’t receive the attention it deserves.

The "aura of exactitude" that often surrounds statistics is one of the main notions that the Points of Significance column will attempt to dispel, while providing useful pointers on using and evaluating statistical measures.
—Dan Evanko, Let's Give Statistics the Attention it Deserves in Biological Research

The column is co-authored with Naomi Altman (Pennsylvania State University). Paul Blainey (Broad) is a contributing co-author.

Free Access

In February 2015, Nature Methods announced that the entire Points of Significance collection will be free.

When Nature Methods launched the Points of Significance column over a year ago we were hopeful that those biologists with a limited background in statistics, or who just needed a refresher, would find it accessible and useful for helping them improve the statistical rigor of their research. We have since received comments from researchers and educators in fields ranging from biology to meteorology who say they read the column regularly and use it in their courses. Hearing that the column has had a wider impact than we anticipated has been very encouraging and we hope the column continues for quite some time.
—Dan Evanko, Points of Significance now free access

Also, in a recent post on the ofschemesandmemes blog, a new statistics collection for biologists was announced.

The pieces range from comments, to advice on very specific experimental approaches, to the entire collection of the Points of Significance columns that address basic concepts in statistics in an experimental biology context. These columns, originally published in Nature Methods thanks to Martin Krzywinski and guest editor Naomi Altman, have already proven very popular with readers and teachers. Finally, the collection presents a web tool to create box plots among other resources.
—Veronique Kiermer, Statistics for biologists—A free Nature Collection

continuity and consistency

Each column is written with continuity and consistency in mind. Our goal is to never rely on concepts that we have not previously discussed. We do not assume previous statistical knowledge—only basic math. Concepts are illustrated using practical examples that embody the ideas without extraneous complicated details. All of the figures are designed with the same approach—as simple and self-contained as possible.

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news + thoughts

Tree of Emotional Life

Sun 17-02-2019

One moment you're :) and the next you're :-.

Make sense of it all with my Tree of Emotional life—a hierarchical account of how we feel.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A section of the Tree of Emotional Life.

Find and snap to colors in an image

Sat 29-12-2018

One of my color tools, the colorsnap application snaps colors in an image to a set of reference colors and reports their proportion.

Below is Times Square rendered using the colors of the MTA subway lines.


Colors used by the New York MTA subway lines.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Times Square in New York City.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Times Square in New York City rendered using colors of the MTA subway lines.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Granger rainbow snapped to subway lines colors from four cities. (zoom)

Take your medicine ... now

Wed 19-12-2018

Drugs could be more effective if taken when the genetic proteins they target are most active.

Design tip: rediscover CMYK primaries.

More of my American Scientific Graphic Science designs

Ruben et al. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine Science Translational Medicine 10 Issue 458, eaat8806.

Predicting with confidence and tolerance

Wed 07-11-2018
I abhor averages. I like the individual case. —J.D. Brandeis.

We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.

Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Predicting with confidence and tolerance. (read)

Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.

Background reading

Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.

4-day Circos course

Wed 31-10-2018

A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Composite of the kinds of images you will learn to make in this course.

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 mkweb.bcgsc.ca
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 mkweb.bcgsc.ca
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 mkweb.bcgsc.ca
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