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PNAS Cover: Earth BioGenome Project

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)
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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)


Talks on Circos and its uses.

Circos course.

Circos in the literature.

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).


VIZBI 2011 Hive Plot Poster.

Introduction to hive plots.

Genome Informatics 2010 talk.

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 Honeywell AMX300LF - Amx Mixing Valve Kit - 3/4 Sweat.

Read the details about the design.

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.

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.

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.

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

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 generates circularly composited views of SQL database schemas

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

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

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

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

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

yesorno (get answers to your problems - just answers)

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 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 is my commercial front-end.

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

UBC model rocket launch competition was not without accidents.

Thu 17-03-2022

My cover design on the 17 March 2022 Nature issue depicts the evolutionary properties of sequences at the extremes of the evolvability spectrum.

My Nature squiggles cover. 17 March 2022. (more)

Vaishnav ED et al. The evolution, evolvability and engineering of gene regulatory DNA (2022) Nature 603 455–463.

Mon 14-03-2022

Celebrate `\pi` Day (March 14th) and finally hear what you've been missing.

“three one four: a number of notes” is a musical exploration of how we think about mathematics and how we feel about mathematics. It tells stories from the very beginning (314…) to the very (known) end of π (...264) as well as math (Wallis Product) and math jokes (Feynman Point), repetition (nn) and zeroes (null).

Listen to `\pi` in the style of 20th century classical music. (details)

The album is scored for solo piano in the style of 20th century classical music – each piece has a distinct personality, drawn from styles of Boulez, Feldman, Glass, Ligeti, Monk, and Satie.

Each piece is accompanied by a piku (or πku), a poem whose syllable count is determined by a specific sequence of digits from π.

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, VINTAGE BUNDY SELMER (H & A) MODEL TROMBONE IN A GOOD CONDITION, 2019 `\pi` Day, 2020 `\pi` Day and 2021 `\pi` Day.

Fri 28-01-2022

My design appears on the 25 January 2022 PNAS issue.

My PNAS cover design captures the vision of the Earth BioGenome Project — to sequence everything. (more)

The cover shows a view of Earth that captures the vision of the Earth BioGenome Project — understanding and conserving genetic diversity on a global scale. Continents from the Authagraph projection, which preserves areas and shapes, are represented as a double helix of 32,111 bases. Short sequences of 806 unique species, sequenced as part of EBP-affiliated projects, are mapped onto the double helix of the continent (or ocean) where the species is commonly found. The length of the sequence is the same for each species on a continent (or ocean) and the sequences are separated by short gaps. Individual bases of the sequence are colored by dots. Species appear along the path in alphabetical order (by Latin name) and the first base of the first species is identified by a small black triangle.

Lewin HA et al. The Earth BioGenome Project 2020: Starting the clock. (2022) PNAS 119(4) e2115635118.

Tue 25-01-2022

As part of the COVID Charts series, I fix a muddled and storyless graphic tweeted by Adrian Dix, Canada's Health Minister.

I show you how to fix color schemes to make them colorblind-accessible and effective in revealing patters, how to reduce redundancy in labels (a key but overlooked part of many visualizations) and how to extract a story out of a table to frame the narrative.

Browse all the COVID charts.

Clear titles introduce the graphic, which starts with informative and non-obvious observations of the relationship between age, number of comorbidities, vaccination status and hospitalization rates. Supporting the story is a tidy table that gives you detailed statistics for each demographic. (more)
Sat 29-05-2021

The Sanctuary Project is a Lunar vault of science and art. It includes two fully sequenced human genomes, sequenced and assembled by us at Canada's Michael Smith Genome Sciences Centre.

The first disc includes a song composed by Flunk for the (eventual) trip to the Moon.

But how do you send sound to space? I describe the inspiration, process and art behind the work.

The song 'Down Here / Moon Above' from Flunk's new album History of Everything Ever is our song for space. It appears on the Sanctuary genome discs, which aim to send two fully sequenced human genomes to the Moon. (more)

Browse the genome discs.

Sun 14-03-2021

Celebrate `\pi` Day (March 14th) and finally see the digits through the forest.

The 26th tree in the digit forest of `\pi`. Why is there a flower on the ground?. (details)

This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.

The first 46 digits of `\pi` in 8 trees. There are so many more. (details)

And things can get crazy in the forest.

A forest of the digits of '\pi`, by ecosystem. (details)

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, New 2020 red toro dingo txl 2000t mini skid steer with attachmen and 2019 `\pi` Day.

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