resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
data visualization + art
The data will stand out—and you will too.
BD Genomics stereoscopic art exhibit — AGBT 2017
Art is science in love.
— E.F. Weisslitz
data in new dimensions
convergence of art, genomics and bioinformatics
In genomics, insights can hinge on a difference of one. One cellular mutation to go from healthy to diseased. One cell migration from tumor to metastasis. Even subtle differences in gene expression between healthy cells shapes their form and function.
In Data in New Dimensions, we’ve created an immersive data art experience celebrating the individuality and often underestimated influence of the single cell—captured by high-throughput single cell analysis.
Using the rich data from the very tools and instruments in this room, we’ve transformed data points back into cells and, informed by their differences, allowed those cells to once again rejoin the world of the viewer in the third dimension.
How do these canvases make you think about the difference of one in your work?
difference of one expression
This piece contrasts two different blood cell states, diseased versus healthy, in such a way that the differences manifest as depth. Cells on the base plane (the closest to the wall) represent healthy control cells, while diseased cells ascend increasingly closer to the viewer based on how different they are from their healthy counterpart.
difference of one migration
This piece paints a picture of the diversity of disease, showing how the cells of a tumor and its metastasis vary in expression patterns. These differences are manifested in the piece through each cell’s position in the third dimension. Cells from the primary tumor exist on the base layer (closest to the wall). Cells from the metastatic site project into the room based on the degree of difference from the nearest primary tumor cell in their cluster.
difference of one function
This piece explores the expression differences that help determine a healthy cell’s role within an organism. Each cluster corresponds to a different cell type along the renal tubule, with that cluster’s depth mapping to its position along the tubule. Blood enters the tubule through the cells on the base layer (closest to the wall) and is filtered by the cells in the successively ascending layers. The remaining waste exits past the cells in the layer nearest to the viewer.
news + thoughts
Tree of Emotional Life
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.
Find and snap to colors in an image
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.
Take your medicine ... now
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
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%).
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
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.
Oryza longistaminata genome cake
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.
