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design + visualization

VIZBI 2012

Visualization Principles Tutorial


This tutorial took place on Monday Mar 5th 2012 at VIZBI 2012 in Heidelberg Germany.

Introduction

Jessie Kennedy · We will present fundamental principles of graphic design and visual communication that will help you create more effective interactive and print visualizations. You will learn how the purposeful use of salience, color, consistency and layout can help communicate large data sets and complex ideas with greater immediacy and clarity.

Cydney Nielsen · We will illustrate how these principles were implemented in ABySS-Explorer to visualize genome assemblies, an example to show you ways to apply design ideas to your own project.

Martin Krzywinski · At the end of the tutorial, you will apply what you have learned in an interactive group session in which you will design a figure illustrating a biological process.

Agenda

Download agenda + participant list

9:30 – 10:15 45 min Jessie Kennedy
Principles
10:15 – 10:25 10 min break
10:25 – 11:10 45 min Cydney Nielsen
Design Process
11:10 – 11:20 10 min form teams + select figure to critique
11:20 – 11:30 10 min break
11:30 – 12:00 30 min Martin Krzywinski
Practical — Breakout session
download papers
12:00 – 13:00 60 min team presentations
Interactive
suggested solutions

It is not necessary to read the paper from which your figure was selected. I have included the papers only if you are interested in learning about the figure's context.

Visualization and Design Resources

Effect of resolution on sequence visualization

Principles of effective color selection

Designing effective visualizations in the biological sciences (PSA Genomics Workshop, Seattle, 12 July 2011)

Circos and Hive Plots: Challenging visualization paradigms in genomics and network analysis (PSA Genomics Workshop, Seattle, 12 July 2011)

Designing effective visualizations in the biological sciences (Genome Sciences Center bioinformatics seminar, 26 August 2011)

Drawing Data: Creaing information-rich, informative and appealing figures for publication and presentation (BCCA workshop, 8 Jun 2011)

Behind a great figure is a design principle (BCB Spring Seminar, Iowa State, 27 Feb 2012)

Visualizing Quantitative Information (Genome Sciences Center bioinformatics seminar)

Blast from the past

Linux and Genomics: Two Revolutions (USENIX 2004)

news + thoughts

Nasa to send our human genome discs to the Moon

Sat 23-03-2024

We'd like to say a ‘cosmic hello’: mathematics, culture, palaeontology, art and science, and ... human genomes.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | A cosmic hello of art, science, and genomes. (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | Benoit Faiveley, founder of the Sanctuary project gives the Sanctuary disc a visual check at CEA LeQ Grenoble (image: Vincent Thomas). (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | Sanctuary team examines the Life disc at INRIA Paris Saclay (image: Benedict Redgrove) (details)

Comparing classifier performance with baselines

Sat 23-03-2024

All animals are equal, but some animals are more equal than others. —George Orwell

This month, we will illustrate the importance of establishing a baseline performance level.

Baselines are typically generated independently for each dataset using very simple models. Their role is to set the minimum level of acceptable performance and help with comparing relative improvements in performance of other models.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Comparing classifier performance with baselines. (read)

Unfortunately, baselines are often overlooked and, in the presence of a class imbalance5, must be established with care.

Megahed, F.M, Chen, Y-J., Jones-Farmer, A., Rigdon, S.E., Krzywinski, M. & Altman, N. (2024) Points of significance: Comparing classifier performance with baselines. Nat. Methods 20.

Happy 2024 π Day—
sunflowers ho!

Sat 09-03-2024

Celebrate π Day (March 14th) and dig into the digit garden. Let's grow something.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2024 π DAY | A garden of 1,000 digits of π. (details)

How Analyzing Cosmic Nothing Might Explain Everything

Thu 18-01-2024

Huge empty areas of the universe called voids could help solve the greatest mysteries in the cosmos.

My graphic accompanying How Analyzing Cosmic Nothing Might Explain Everything in the January 2024 issue of Scientific American depicts the entire Universe in a two-page spread — full of nothing.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
How Analyzing Cosmic Nothing Might Explain Everything. Text by Michael Lemonick (editor), art direction by Jen Christiansen (Senior Graphics Editor), source: SDSS

The graphic uses the latest data from SDSS 12 and is an update to my Superclusters and Voids poster.

Michael Lemonick (editor) explains on the graphic:

“Regions of relatively empty space called cosmic voids are everywhere in the universe, and scientists believe studying their size, shape and spread across the cosmos could help them understand dark matter, dark energy and other big mysteries.

To use voids in this way, astronomers must map these regions in detail—a project that is just beginning.

Shown here are voids discovered by the Sloan Digital Sky Survey (SDSS), along with a selection of 16 previously named voids. Scientists expect voids to be evenly distributed throughout space—the lack of voids in some regions on the globe simply reflects SDSS’s sky coverage.”

voids

Sofia Contarini, Alice Pisani, Nico Hamaus, Federico Marulli Lauro Moscardini & Marco Baldi (2023) Cosmological Constraints from the BOSS DR12 Void Size Function Astrophysical Journal 953:46.

Nico Hamaus, Alice Pisani, Jin-Ah Choi, Guilhem Lavaux, Benjamin D. Wandelt & Jochen Weller (2020) Journal of Cosmology and Astroparticle Physics 2020:023.

Sloan Digital Sky Survey Data Release 12

constellation figures

Alan MacRobert (Sky & Telescope), Paulina Rowicka/Martin Krzywinski (revisions & Microscopium)

stars

Hoffleit & Warren Jr. (1991) The Bright Star Catalog, 5th Revised Edition (Preliminary Version).

cosmology

H0 = 67.4 km/(Mpc·s), Ωm = 0.315, Ωv = 0.685. Planck collaboration Planck 2018 results. VI. Cosmological parameters (2018).

Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA
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