Tango is a sad thought that is danced.think & dancemore quotes

# at a glance

The Outbreak Poems — artistic emissions in a pandemic

# Circos

Circos is software that generates circularly composited views of genomic data and annotations.

Circos is a tool for visualizing data in a circular layout. It is widely used in genomics and cancer biology, but can show any kind of data. (Learn more)

Figures created by Circos are engaging, pretty and informative.

Many kind of data tracks are supported. Shown here is a small sample: links, tiles and heatmaps. (Learn more)

Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. (presentations on Circos; drawn heavily from Tufte's Visual Display of Quantitative Information)

Data display can be automated to show a large number of tracks. (Learn more)

## RESOURCES

Talks on Circos and its uses.

Circos course.

Circos in the literature.

# Hive Plots

Hive plots are a type of layout algorithm that is designed to make sense out of very large networks. The method is quantitative — placement of nodes depends only on network properties.

In a hive plot, nodes are placed on linear axes, which are arranged radially. Nodes are mapped to axis based on topology (e.g. connectivity) or user categories. Network edges are shown as links between axis node points, and can be colored further by additional metadata.

Hive plots are an answer to the challenge of uninformative network hairball visualization.

In a hive plot, nodes are placed on linear axes, which are arranged radially. Nodes are mapped to axis based on topology (e.g. connectivity) or user categories. Network edges are shown as links between axis node points, and can be colored further by additional metadata.

Hive plots are excellent at showing alignments between more than two genomes. (High resolution on white or black)

Hive plots are excellent at comparing ratios. Here each panel shows 24 ratios (8 between each axis pair).

## RESOURCES

VIZBI 2011 Hive Plot Poster.

Introduction to hive plots.

Genome Informatics 2010 talk.

# Genome Informatics Cover

I had the opportunity to design the cover of the Genome Informatics Conference program book. The cover shows sequences of some of the genes and viruses that appear in this conference's abstracts and uses the genome path algorithm previously used in the Deadly Genomes poster.

# Deadly Genomes — Run Away

The Deadly Genomes is a visualization of the size and structure of genomes of viruses and bacteria that are agents of prevalent human diseases. Their genomes are visualized as a path, and each organism is spaced on the poster according to the incidence and mortality of the disease.

This image reached the finalist stage at the 2009 National Science Foundation Visualization Challenge.

# Our 10 year anniversary

December 2009 saw the 10th Anniversary of the Genome Sciences Center. Some commemorative swag was handed out, among which was a stainless steel water bottle with the following image.

The image contains a barcode called QR Code (learn more) which encodes the names of all current employees at the Center.

# Visualizing Debates

Lexical analysis of 2008 US Presidential and Vice-Presidential Debates indicates that the speech patterns between candidates (especially those paired in a debate) are extremely similar and that the complexity of vice-presidential candidates is lower than presidential candidates (uniqueness is lower, repetition is higher).

Palin has the longest sentences, Biden repeats himself the most and has the smallest vocabulary, while patterns for Obama and McCain are eerily similar.

Use Atom feeds of candidates' word lists to create Wordles.

# Optimizing Keyboard Layouts - carpalx

carpalx is a keyboard optimizer which rearranges letter positions on a keyboard to minimize typing effort. Discover the magical XBUL keyboard layouts which minimizes typing of English text. Or, if you dare, venture into the land of the disfigured TNWCLR keyboard layout which makes typing English text excruciatingly painful.

# High Dynamic Time Range Photography (HDTR)

High Dynamic Time Range images (HDTR) are single-frame composites of a set of time-lapse photos.

# Perl Workshops

The bioinformatics Perl workshop offers courses to help you learn Perl and apply it to your work. We have courses on introductory Perl, intermediate Perl, and others. Learn how to use map, grep and sort more efficiently or how to perform data analysis at the command line. The workshop is open to the public (given at the GSC 570 W 7th location) and all slides from each lecture are available online.

# schemaball

schemaball generates circularly composited views of SQL database schemas

# BAC Arrays

High-resolution 32k BAC array for aCGH studies of human genome.

# clusterpunch

clusterpunch is a mini-benchmarker for clusters designed to monitor availability of resources

# port knocking

portknocking is a network authentication method in which a client establishes a connection to a host which presents no open ports

# Life of Alex

alex is a very famous pet rat, who had appearances in Genome Research and Maximum PC.

# Tuple Color Encoding

color encoding of vectors Color::TupleEncode - Mapping tuples to colors and visually comparing numbers

# Genome Coverage Tables

short-read sequencing genome coverage tables tables of read coverage for haploid, diploid and triploid genomes for a given sequencing redundancy

genome coverage simulator explore whole genome shotgun statistics

# Image Color Summarizer

Image color summarizer produces statistics about an image's mean/median hue, saturation and intensity values. It's fun to play with and can be (eventually) used to auto-tag images based on color content.

# Lumondo Photography

Lumondo Photography is my commercial front-end.

# Canon Lenses

Canon EF Lenses A f/ vs mm chart of all Canon EF lenses, and a few links to useful lens resources.

# UBC Rockets

UBC model rocket launch competition was not without accidents.

# Points of Significance celebrates 50th column

Mon 24-08-2020

We are celebrating the publication of our 50th column!

To all our coauthors — thank you and see you in the next column!

Nature Methods Points of Significance: Celebrating 50 columns of clear explanations of statistics. (read)

# Uncertainty and the management of epidemics

Mon 24-08-2020

When modelling epidemics, some uncertainties matter more than others.

Public health policy is always hampered by uncertainty. During a novel outbreak, nearly everything will be uncertain: the mode of transmission, the duration and population variability of latency, infection and protective immunity and, critically, whether the outbreak will fade out or turn into a major epidemic.

The uncertainty may be structural (which model?), parametric (what is $R_0$?), and/or operational (how well do masks work?).

This month, we continue our exploration of epidemiological models and look at how uncertainty affects forecasts of disease dynamics and optimization of intervention strategies.

Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (read)

We show how the impact of the uncertainty on any choice in strategy can be expressed using the Expected Value of Perfect Information (EVPI), which is the potential improvement in outcomes that could be obtained if the uncertainty is resolved before making a decision on the intervention strategy. In other words, by how much could we potentially increase effectiveness of our choice (e.g. lowering total disease burden) if we knew which model best reflects reality?

This column has an interactive supplemental component (download code) that allows you to explore the impact of uncertainty in $R_0$ and immunity duration on timing and size of epidemic waves and the total burden of the outbreak and calculate EVPI for various outbreak models and scenarios.

Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Uncertainty and the management of epidemics. Nature Methods 17.

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.

# Cover of Nature Genetics August 2020

Mon 03-08-2020

Our design on the cover of Nature Genetics's August 2020 issue is “Dichotomy of Chromatin in Color” . Thanks to Dr. Andy Mungall for suggesting this terrific title.

Dichotomy of Chromatin in Color. Nature Genetics, August 2020 issue. (read more)

The cover design accompanies our report in the issue Gagliardi, A., Porter, V.L., Zong, Z. et al. (2020) Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes. Nature Genetics 52:800–810.

# Poster Design Guidelines

Wed 15-07-2020

Clear, concise, legible and compelling.

The PDF template is a poster about making posters. It provides design, typography and data visualiation tips with minimum fuss. Follow its advice until you have developed enough design sobriety and experience to know when to go your own way.

Poster Design Guidelines — Clear, concise, legible and compelling..

# The SEIRS model for infectious disease dynamics

Thu 18-06-2020

Realistic models of epidemics account for latency, loss of immunity, births and deaths.

We continue with our discussion about epidemic models and show how births, deaths and loss of immunity can create epidemic waves—a periodic fluctuation in the fraction of population that is infected.

Nature Methods Points of Significance column: The SEIRS model for infectious disease dynamics. (read)

This column has an interactive supplemental component (download code) that allows you to explore epidemic waves and introduces the idea of the phase plane, a compact way to understand the evolution of an epidemic over its entire course.

Nature Methods Points of Significance column: The SEIRS model for infectious disease dynamics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

# Gene Machines

Fri 05-06-2020

Shifting soundscapes, textures and rhythmic loops produced by laboratory machines.

In commemoration of the 20th anniversary of Canada's Michael Smith Genome Sciences Centre, Segue was commissioned to create an original composition based on audio recordings from the GSC's laboratory equipment, robots and computers—to make “music” from the noise they produce.

Gene Machines by Segue. Now available on vinyl.

# 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