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.

Read the details about the design.

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

Yes or No

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

Typography

Letters - Introduction to Typography (PDF)

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.

Flickr stream

A collection of my photos on flickr

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.

Visualizing an MMRPG Class

I am a warden.