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.
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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.
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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.
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Learn more)
RESOURCES
▲ Talks on Circos and its uses.
▲ 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
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▲ 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.
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.
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.
schemaball generates circularly composited views of SQL database schemas
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.
yesorno (get answers to your problems - just answers)
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.
Canon EF Lenses A f/ vs mm chart of all Canon EF lenses, and a few links to useful lens resources.
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.
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Browse the genome discs.
Sun 30-05-2021
All that glitters is not gold. —W. Shakespeare
The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.
We discuss the positive predictive value (PPV) and how practices such as screen can increase it.
Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18:224–225.
Tue 09-02-2021
We demand rigidly defined areas of doubt and uncertainty! —D. Adams
A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.
Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.
▲ Nature Methods Points of Significance column: Standardization fallacy.
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Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.
Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.
Fri 13-11-2020
Clear, concise, legible and compelling.
Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.
▲ Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.
Tue 06-10-2020
An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.
▲ A poster of high BMI and obesity prevalence for 185 countries.
