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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

Propensity score matching

Mon 16-09-2024

I don’t have good luck in the match points. —Rafael Nadal, Spanish tennis player

In many experimental designs, we need to keep in mind the possibility of confounding variables, which may give rise to bias in the estimate of the treatment effect.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Propensity score matching. (read)

If the control and experimental groups aren't matched (or, roughly, similar enough), this bias can arise.

Sometimes this can be dealt with by randomizing, which on average can balance this effect out. When randomization is not possible, propensity score matching is an excellent strategy to match control and experimental groups.

Kurz, C.F., Krzywinski, M. & Altman, N. (2024) Points of significance: Propensity score matching. Nat. Methods 21:1770–1772.

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

Fri 22-03-2024

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 imbalance, 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 21:546–548.

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)
Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA
Google whack “vicissitudinal corporealization”
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