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# information: fun

UCD Computational and Molecular Biology Symposium, Dublin, Ireland. 1-2 Dec 2016.

# EMBO Journal 2011 Cover Contest

## non-scientific image entry - fiber optics - honourable mention

For the EMBO Journal 2011 Cover Contest, I prepared two entries, one for the scientific category and one for the non-scientific category.

The non-scientific entry is abstract photo of fiber optics. The scientific entry was an information graphic showing a hive panel of genomic annotations in human, mouse and dog genomes. The hive panel is based on the use of the newly introduced hive plot.

## About the EMBO Journal Cover Contest

The EMBO Journal non-scientific cover prize is awarded for the most interesting and beautiful image made outside the lab. Contestants may submit, for example, photos or artistic impressions of wildlife animals, plants or landscapes. Particularly welcome will also be hand or computer-generated paintings or drawings (or photographs of other works of art) related to a biological or molecular biological topic.

The EMBO Journal scientific cover prize is awarded for the most captivating and thought-provoking contribution depicting a piece of molecular biology research. Entries can include light or electron micrographs, 3D reconstructions or models of biological specimen or molecules, spectacular artefacts collected in the lab, original new views of lab equipment (but not of colleagues!), or other research-based images to be of interest to molecular biologists.

Examples of scientific cover image winners from previous years. My Circos image (top left) won the 2010 scientfic image cover category. (see more)

## 2011 Contest and Image Status

The 2011 winners have been announced. The scientific image winner was Heiti Paves, who submitted a confocal image of an Arabidopsis thaliana anther filled with pollen grains. The non-scientific winner was Dieter Lampl, with his "Blue Ice" photo — a glacier in Los Glaciares National Park in Patagonia.

My non-scientific entry (photo of fiber optics) received honourable mention and was included in the Favourites of the Jury gallery.

## non-scientific image entry - fiber Optics

Four genomes — The illustration, originally part of a poster, shows syntenic relationships between human, chimpanzee, mouse and zebrafish genomes. Curved links encode sequence similarity and outer data tracks represent consensus similarity statistics and orthologous genes. The cover image shows a detail of a visualization prepared with the free genome comparison tool, Circos. (EMBO Journal - Best Scientific Cover - 2010)
My 2011 non-scientific fiber optic entry appears in a gallery of a small selection of images that were shortlisted by the jury of The EMBO Journal Cover Contest 2011. Images were selected with the aim of highlighting the diversity and quality of submissions in both, the scientific and non-scientific categories of the contest. (view gallery)

My non-scientific entry was an abstract image photo of fiber optics. It received honourable mention and were included in the Favourites of the Jury gallery.

The motivation and technical details behind these photos are described here.

The other entry, a scientific image, was an information graphic showing a hive panel of genomic annotations in human, mouse and dog genomes, based on the use of the newly introduced hive plot.

My submission of a large Circos figure for its cover (see right), which was originally designed for a poster that introduced Circos, was awarded the 2010 EMBO Journal best scientific cover prize.

## entry details

Some time ago, I did a personal project of photos of fiber optic strands. These worked out well. I had not done anything with these images, and thought they would make a competitive entry into the cover contest.

My first attempt at photographing fiber optic lamp strands. These images were bundled into a set called Diving Horror, because of their likeness to creepy tentacles of creatures of the deep. (more images on flickr.)

I revisited the fiber optic lamp with a higher resolution camera (Canon 5D — original images were from a Canon 20D) and a dedicated macro lens (Sigma 150mm f2.8 EX APO DG HSM Macro) (original images were shot with the Canon EF 24-70L).

From these new images, shown below, I created five EMBO Journal cover submissions.

Second attempt at photographing fiber optic lamp strands. (more images on flickr.)

The submissions would render on the cover as shown below.

Photos of fiber optic lamp strands. (More images on flickr.)

## 2011 EMBO Journal cover contest — fiber optic lamp submission images

2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands. (More images on flickr.)

2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands. (More images on flickr.)

2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands. (More images on flickr.)

2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands. (More images on flickr.)

2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands. (More images on flickr.)

VIEW ALL

# Intuitive Design

Thu 03-11-2016

Appeal to intuition when designing with value judgments in mind.

Figure clarity and concision are improved when the selection of shapes and colors is grounded in the Gestalt principles, which describe how we visually perceive and organize information.

One of the Gestalt principles tells us that the magenta and green shapes will be perceived as as two groups, overriding the fact that the shapes within the group might be different. What the principle does not tell us is how the reader is likely to value each group. (read)

The Gestalt principles are value free. For example, they tell us how we group objects but do not speak to any meaning that we might intuitively infer from visual characteristics.

Nature Methods Points of View column: Intuitive Design. (read)

This month, we discuss how appealing to such intuitions—related to shapes, colors and spatial orientation— can help us add information to a figure as well as anticipate and encourage useful interpretations.

Krzywinski, M. (2016) Points of View: Intuitive Design. Nature Methods 13:895.

# Regularization

Fri 04-11-2016

Constraining the magnitude of parameters of a model can control its complexity.

This month we continue our discussion about model selection and evaluation and address how to choose a model that avoids both overfitting and underfitting.

Ideally, we want to avoid having either an underfitted model, which is usually a poor fit to the training data, or an overfitted model, which is a good fit to the training data but not to new data.

Nature Methods Points of Significance column: Regularization (read)

Regularization is a process that penalizes the magnitude of model parameters. This is done by not only minimizing the SSE, $\mathrm{SSE} = \sum_i (y_i - \hat{y}_i)^2$, as is done normally in a fit, but adding to this minimized quantity the sum of the mode's squared parameters, $\mathrm{SSE} + \lambda \sum_i \hat{\beta}^2_i$.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Regularization. Nature Methods 13:803-804.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Model Selection and Overfitting. Nature Methods 13:703-704.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Classifier evaluation. Nature Methods 13:603-604.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Logistic regression. Nature Methods 13:541-542.

# 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