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Trance opera—Spente le Stellebe dramaticmore quotes

Visualizaiton workshop at UBC B.I.G. Research Day. 11 May 2016


writing

Writing

Poetry

Inked Sadness is a collection of poems written in that difficult time between being no longer young, but not yet old.

Expressions and Conversations of Love are short heart-breakers.

Scripts

Proverbial Man considers how our names and expectations limit our perceptions and freedoms. No answers are offered. I don't think I finished this.

The Surrogate echoes my own fears of fleeing from Poland in the early 80s. Or at least the fears I retroactively erected, to add drama. Count on the Polish for drama.

Narrative

Thirty Reasons should be enough to decide a place isn't worth returning to.

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news + thoughts

Pathways

Mon 04-01-2016

Apply visual grouping principles to add clarity to information flow in pathway diagrams.

We draw on the Gestalt principles of connection, grouping and enclosure to construct practical guidelines for drawing pathways with a clear layout that maintains hierarchy.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of View column: Pathways. (read)

We include tips about how to use negative space and align nodes to emphasizxe groups and how to effectively draw curved arrows to clearly show paths.

Hunnicutt, B.J. & Krzywinski, M. (2016) Points of Viev: Pathways. Nature Methods 13:5.

background reading

Wong, B. (2010) Points of Viev: Gestalt principles (part 1). Nature Methods 7:863.

Wong, B. (2010) Points of Viev: Gestalt principles (part 2). Nature Methods 7:941.

...more about the Points of View column

Multiple Linear Regression

Mon 04-01-2016

When multiple variables are associated with a response, the interpretation of a prediction equation is seldom simple.

This month we continue with the topic of regression and expand the discussion of simple linear regression to include more than one variable. As it turns out, although the analysis and presentation of results builds naturally on the case with a single variable, the interpretation of the results is confounded by the presence of correlation between the variables.

By extending the example of the relationship of weight and height—we now include jump height as a second variable that influences weight—we show that the regression coefficient estimates can be very inaccurate and even have the wrong sign when the predictors are correlated and only one is considered in the model.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Multiple Linear Regression. (read)

Care must be taken! Accurate prediction of the response is not an indication that regression slopes reflect the true relationship between the predictors and the response.

Altman, N. & Krzywinski, M. (2015) Points of Significance: Multiple Linear Regression Nature Methods 12:1103-1104.

Background reading

Altman, N. & Krzywinski, M. (2015) Points of significance: Simple Linear Regression Nature Methods 12:999-1000.

...more about the Points of Significance column

Circos and Hive Workshop Workshop—Poznan, Poland

Sun 13-12-2015

Taught how Circos and hive plots can be used to show sequence relationships at Biotalent Functional Annotation of Genome Sequences Workshop at the Institute for Plant Genetics in Poznan, Poland.

Students generated images published in Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis.

Workshop materials: slides, handout, Circos and hive plot files.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Drawing synteny between modern and ancient genomes with Circos.

Students also learned how to use hive plots to show synteny.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hive plots are great at showing 3-way sequence comparisons. Here three modern species of Australian Brassicaceae (S. nutans, S. lineare, B. antipoda) are compared based on their common relationships to the ancestral karotype.

Mandakova, T. et al. Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis The Plant Cell, Vol. 22: 2277-2290, July 2010

Play the Bacteria Game

Mon 14-12-2015

Choose your own dust adventure!

Nobody likes dusting but everyone should find dust interesting.

Working with Jeannie Hunnicutt and with Jen Christiansen's art direction, I created this month's Scientific American Graphic Science visualization based on a recent paper The Ecology of microscopic life in household dust.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An analysis of dust reveals how the presence of men, women, dogs and cats affects the variety of bacteria in a household. Appears on Graphic Science page in December 2015 issue of Scientific American.

We have also written about the making of the graphic, for those interested in how these things come together.

This was my third information graphic for the Graphic Science page. Unlike the previous ones, it's visually simple and ... interactive. Or, at least, as interactive as a printed page can be.

More of my American Scientific Graphic Science designs

Barberan A et al. (2015) The ecology of microscopic life in household dust. Proc. R. Soc. B 282: 20151139.


me as a keyword list

aikido | analogies | animals | astronomy | comfortable silence | cosmology | dorothy parker | drumming | espresso | fundamental forces | good kerning | graphic design | humanism | humour | jean michel jarre | kayaking | latin | little fluffy clouds | lord of the rings | mathematics | negative space | nuance | perceptual color palettes | philosophy of science | photography | physical constants | physics | poetry | pon farr | reason | rhythm | richard feynman | science | secularism | swing | symmetry and its breaking | technology | things that make me go hmmm | typography | unix | victoria arduino | wine | words