Distractions and amusements, with a sandwich and coffee.
With some very smart people, I work on problems in data visualization applied to cancer research and genome analysis. Previously I was involved in fingerprint mapping, system administration, computer security, fashion photography, medical imaging and LHC particle physics. My work is guided by a need to rationalize, make things pretty, combine science with art, mince words, find good questions and help make connections between ideas. All while exercising snark.
Circos is software that generates circularly composited views of genomic data and annotations.
Figures created by Circos are engaging, pretty and informative.
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)
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.
Hive plots are an answer to the challenge of uninformative network hairball visualization.
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.
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.
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
color encoding of vectors Color::TupleEncode - Mapping tuples to colors and visually comparing numbers
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.
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.
An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.
Building on the method I used to analyze the 2008, 2012 and 2016 U.S. Presidential and Vice Presidential debates, I explore word usagein the 2020 Debates between Donald Trump and Joe Biden.
We are celebrating the publication of our 50th column!
To all our coauthors — thank you and see you in the next column!
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.
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.
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.
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.
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.