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fun + amusement
The New Clock - A Proposal
the standard clock
Consider the lowly wall clock. It's practical: it generally tells the correct time. It's the same clock everywhere and after a while (like now) that gets boring pretty quickly.
In the regular clock the face bezels stay in place and the hands move. Why am I telling you this? Well, maybe you see where I'm going.
the non-standard clock
Instead of rotating hands and a stationary bezel, consider the clock with stationary hands and a rotating bezel.
In the non-standard clock there are two independent bezels and two independent hands. The bezels rotate counterclockwise to simulate the standard clockwise motion of the hands. Note the word simulate here. The hands are not moving. (Applying some Galilean relativity, in the frame of reference of the hands, it's the bezels that are rotating. The non-standard clock simply takes the frame of reference of the hands, not the bezel).
IT'S LIKE
Some watches (esp. divers' watches) already implement a rotating bezel to mark elapsed time; some have an extra racheting mechanism for safety.
FEATURE
the bezel can move clockwise if you like - you just have to reprogram the clock.
telling time on the non-standard clock
To tell the time on the non-standard clock is a process identical to using the standard clock. You look at the bezel numbers at the ends of the hour and minute hands
On the fixed bezel layout, most people will take a short cut and tell the time by the position of the hands. This works as long as you have a standard clock. On a non-standard clock the position of the hands is insufficient.
Here is a non-standard clock telling us it is 4:15. You know this because the minute hand (black) points to 15 on the minute bezel (inner bezel) and the hour hand (red) points to just after 4 on the hour bezel (outer).
After 15 minutes, it's 4:30 and our non-standard clock bezels have moved a little bit.
It is now 5:00.
Can you tell what time it is on the non-standard clock below?
customizing the non-standard clock
Customizing your non-standard clock is easy. Simply adjust the hands to desired positions and set the time by moving the bezels. The clock below shows the same time as the clock in the above figure — both show 8:50.
TIP :: spice it up with multiple non-standard clocks side-by-side with different hand positions.
TIP
Set both hand positions to 12 o'clock and then remove the hands; to tell time, read the numbers on the hour and minute bezels at the apex of the clock.
EXTENSION
Sophisticated implementations of the non-standard clock could periodically randomize hand positions to keep things interesting; by the time you've figured out the time in the morning, you're wide awake.
hardware implementation
If you would like to implement the non-standard clock, I would be happy to hear from you. One should be able to take a regular wall clock, reverse the direction of the hand mechanism and rig a freely moving bezel to each of the minute and hour mechanism. The hands should not move and can be fixed to the front glass plate, for example.
conclusions
It should now be clear that the non-standard clock is superior to the standard clock. The reasons are
- it's much harder to tell time on the non-standard clock, which makes your brain do more work
- COROLLARY :: it will confuse everyone
- COROLLARY :: you have a great excuse for being late
- you can customize your own non-standard clock by moving the hands to arbitrary locations
- COROLLARY :: two non-standard clocks can have their hands and bezels at different positions but still be telling the same time
news + thoughts
Figure Design and Writing — Two Goals, One Process
This month I look at how creating effective figures is similar to the process of writing well in the Points of View column Elements of Visual Style.
Using Strunk's Elements of Style as an example of writing guidelines, I look how these can be translated to creating figures.
VIZBI 2013 Keynote—Visual Design Principles
When we create figures, we must communicate and design. In my talk I discuss some of the rules that turn graphical improvisation into a structured and reproducible process.
The fractal tree was created with OneZoom, which received the best poster award at the conference.
Happy Pi Day— 3.14
Celebrate Pi Day (March 14th) with a funky modern posters. Transcend, don't repeat, yourself and watch the dots shimmer.
The posters were inspired by the beautiful AIDS posters by Elena Miska.
For the Love of Type
I am always drawn to type and periodically I must do something about it.
If you were a type, what type would you be? Me, Gill Sans on weekdays and Perpetua on the weekend.
Return of Nature Methods Points of View
I take over from Bang Wong as primary contributor to the Points of View column, a monthly advice and opinion piece about data visualization and information and figure design in molecular biology.
Nature Encode Explorer
Nature's special issue dedicated to the Encode Project uses the Circos motif on its cover as well as the interactive Encode Explorer, which is available as an app at iTunes.
Bloomberg Businessweek Design Conference
Together with Alberto Cairo, and then in conversation with Sam Grobart, I presented about science and design at Bloomberg's Businessweek Design Conference in San Francisco.
ICDM2012 Keynote — Needles in Stacks of Needles
My ICDM2012 keynote on genomics and data mining: Needles in Stacks of Needles.
Genome Research cover
Creating strings of genome jewelery. Read about how it was done.
The design accompanies Cydney Nielsen's Spark manuscript, which appeared in Genome Research.
Biovis 2012 — Getting into Visualization of Large Biological Data Sets
Guidelines for data encoding and visualization in biology, presented presented at Biovis 2012 (Visweek 2012).
2012 Presidential Debates — a Lexical Analysis
Building on the method I used to analyze the 2008 debates, I look at the 2012 Debates between Obama and Romney, lexically speaking. Obama speaks to "folks", while Romney fearmongers with "kill" and "hurt".
Trends in Genetics cover
Making things round, not square. Read about how it was done.
A Circos-based design for the cover of the human genetics special issue of Trends in Genetics (Trends in Genetics October 2012, 28 (10)).
Schloss Dagstuhl - Visualization: communicating, clearly
My talk — Visualization: communicating, clearly from the Biological Data Visualization seminar at Schloss Dagstuhl.
Science needs words
And usually, really long and funny ones.
My neologisms were picked up by James Gorman of the New York Times in an article Ome, the sound of the scientific universe expanding.
PNAS cover
Biology or astrophysics? Read about how it was done.
The image was published on the cover of PNAS (PNAS 1 May 2012; 109 (18))
the art of numbers
Numerology is bogus but art based on numbers has a beautiful random quality. Oh, and none of the metaphysical baggage.
accidental similarity number
The quantity formed by the overlap of two or more numbers.
the 4ness of pi
How much 4ness does π have?
Compare the iness of π to that of the other famous transcendental number, e, and the mysterious but attractive Golden Ratio, φ.
ASCII Illustration—Outer Space, Sequence and Typography
I have found a way to combine my curiosity about space, fear of large sequence assemblies and love of typography in a single illustration. Inspired by typographical portraits, I wanted to automate representing an image with multiple font weights, while sampling characters from a quote or debate transcripts.
Tangering Tango—Color of 2012
If you made widgets, you could be justified in campaigning a widget of the year. Business acumen suggests it should be one of your widgets. Pantone has done exactly that, naming their 17-1463 color (tangerine tango), as color of the year 2012.
I prefer green—green jive.
World's Most Expensive Photograph
I really like the world's most expensive photograph, Rhein II by Andreas Gursky. Cautious use of the word "expensive" should be practised — in this case, merely meaning that only one person saw the $4.3 million price tag. Others saw lower prices, or no price tag at all.
Here's my own attempt at such compositions.
Adobe Swatches for Brewer Palettes
I could not find Illustrator swatch files for this awesome color resource, so I created them myself.
If you're interested in color and design and don't know about Brewer palettes, see my presentation.
Global Visualization of Google Searches by Language
World-wide Google searches, categorized by one of 21 languages, are visualized with WebGL, available from Chrome Experiments. The data offers some fascinating insights such as (a) in what two places in the US are Google searches in Chinese are performed? (b) what are the most remote locations are from which Google searches were detected? (c) Why is Istanbul the 3rd top location for searches? Why is Miami in the top 10?
PSA Genomics Workshop Slides
Designing effective visualizations in the biological sciences.
Circos and Hive Plots: Challenging visualization paradigms in genomics and network analysis.
Tor tor & Loa Loa — 546 Organisms with Same Genus and Species
In a recent conversation, I was challenged to name as many organisms with the same genus and species as I could. Neither a biologist, and especially not a taxonomist, my responses were limited to organisms with sequenced genomes I had come across in the literature. Immediately to mind sprung Gallus gallus (chicken) and ... nothing else. Well, that was embarrassing.
I was suddently taken up by the urge to find all instances of this occurrence. Using resources at the NCBI Taxonomy Browser I downloaded the NCBI taxonomy table which contains 1,097,405 entries in the names.dmp file (not all of these are unique genus/species combinations).
To my suprise I discovered that my performance in this challenge was beyond dysmal. In fact, there are 380 genuses which contain organisms that have the same genus and species name. Most of them (317) include a single organism, but some have many. For example the genus Salamandra has 14 organisms with the species salamandra, including Salamandra salamandra, Salamandra salamandra crespoi and Salamandra salamandra morenica. The genus Regulus has 13 organisms, including Regulus regulus azoricus, Regulus regulus japonensis and Regulus regulus regulus (these are all Goldcrests).
In total, there are 546 unique entries, when organisms with a unique subspecies name are considered distinct. If subspecies is not considered, the number of organisms with the same genus as species (i.e., regardless of subspecies) is 383. Here are organisms whose genus/species name is shorter than 6 letters (82 entries).
Shortest Species/Genus Duplicates (82, 5 letters or less)
Agama agama, Alces alces, Alle alle, Alosa alosa, Anser anser, Appia appia, Apus apus, Arita arita, Arius arius, Aroma aroma, Axis axis, Badis badis, Bagre bagre, Bison bison, Boops boops, Brama brama, Bubo bubo, Bufo bufo, Bulla bulla, Buteo buteo, Butis butis, Catla catla, Chaca chaca, Conta conta, Crex crex, Cynea cynea, Dama dama, Dario dario, Diuca diuca, Dives dives, Ensis ensis, Equus equus, Ficus ficus, Gemma gemma, Gesta gesta, Glis glis, Gobio gobio, Grus grus, Guira guira, Gulo gulo, Hara hara, Hucho hucho, Huso huso, Indri indri, Irus irus, Juga juga, Labeo labeo, Lima lima, Loa loa, Lota lota, Lutra lutra, Lynx lynx, Meles meles, Melo melo, Meza meza, Mitu mitu, Mola mola, Molva molva, Mops mops, Myaka myaka, Naja naja, Nasua nasua, Papio papio, Pauxi pauxi, Perna perna, Pica pica, Pipa pipa, Pipra pipra, Plica plica, Rapa rapa, Rita rita, Sarda sarda, Sisko sisko, Solea solea, Sula sula, Suta suta, Tinca tinca, Todus todus, Tor tor, Uncia uncia, Vimba vimba, Volva volva.Longest Species/Genus Duplicates (5, 14 letters or more)
Coccothraustes coccothraustes
Labiostrongylus labiostrongylus
Macrobilharzia macrobilharzia
Macropostrongylus macropostrongylus
Xanthocephalus xanthocephalus
The nematode worm Macropostrongylus macropostrongylus has the honour of being the longest genus/species duplicate organism. Given this distinction, it is surprising that Pubmed returns only 2 papers that refer to it.
Dataset
Download the full list. The number next to each ENTRY field is the NCBI Taxonomy ID for the organism. In a small number of cases there are ambiguities in parsing the data file (e.g. Troglodytes cf. troglodytes PS-2, Troglodytes sp. troglodytes PS-1). I left these in.
Visual Acuity and Sequence Visualization
Visual acuity limits of the human eye restrict the resolution at which we can comfortably visualize data.
In this short guide, I explain why dividing a scale into no more than 500 divisions is a good idea.
2011 EMBO Journal Cover Contest
For the EMBO Journal 2011 Cover Contest, I prepared two entries, one for the scientific category and one for the non-scientific category.
The 2011 winners have been announced. My non-scientific entry (photo of fiber optics) received honourable mention and was included in the Favourites of the Jury gallery.
New Circos Domains
Until now, Circos did not have its own domain name, having been served from the lengthy and boring http://mkweb.bcgsc.ca/circos.
Recently, I was surprised to find out that the following domains were available
All these now point to the Circos site.
ee spammings - beautiful language of spam poetry
ee spammings are spam edited into a format reminiscent of the poetry of ee cummings. Unwanted solicitations for questionable endeavours and products suddenly turn into heady words of the new literature. Art suddenly freed from the husk of spam.
Literature 2.0 — from unlikely origins.
Here's one example that emphasizes that today is ok.
i got
to touch you
i like us
and know the more.
believe
recontact
me
today ok!
but matters
waiting for
happy
I now have over 20 ee spammings — enjoy them all.
Neologisms - New Words, Much Needed
What do inconversible, mystific, postpetizer, prenopsis and suscitate have in common?
They are words that don't exist, but should. Learn new words.
World's Most Popular Questions
Today's Zeitgeist
What are the world's top questions?
Using Google's autocomplete feature, I have tabulated the world's most popular questions. By combining a interrogative term, such as what, who or why, with a term from a related set, such as do I, can I, and can't I, it is possible to sample the space of questions and obtain the most popular for a given start word combination.
I have tabulated the most popular questions by category.
| general | limits & desires |
| love | money |
| career & education | health |
| sizes & extremes | religion & faith |
Science
What kind of questions about science are people asking? From the Career & Education section,
- Can biology lead to new theorems?
- Can physics explain miracles?
- Can math be fun?
- Can science and religion coexist?
- Can history repeat itself?
- Can psychology be morally neutral?
Curios
What are the strangest questions? I'll let you explore, but these have me wondering:
- Has the world gone mad or is it me?
- Why can't I hold all these limes?
- What happens if I make a formal commitment to Satan?
- Why can't I sell my kidney?
- Who is the most powerful Jedi?
- Can Jesus microwave a burrito?
- Where is the hardest part of your head?
Circos Table Browser
Circos can be used to visualize tabular data, such as spreadsheets.
1,000s of tables have already been visualized. Has yours?
648 Ratios
Hive plots are excellent at visualizing ratios. They're not just an anti-hairball network visualization agent.
Below are visualized 3 x 8 x 27 = 648 (axes, ribbons, plots) ratios visualized.
The image above compares the relative ratios of region annotations in human, mouse and dog genomes.
Cáceres Creativa - Model and Strategy for Urban Innovation
Cáceres is a small city of 100,000 inhabitants in western Spain, where the city government is promoting Cáceres Creativa, a project to build citizens collaboratively sustainable future for the city based on activating the creative capacity of the population.
The project has been published as a book (excerpt), which provides a basis for working with city residents and businesses in this collaborative design.
Circos proved useful in showing the complex relationships that are established in such an environment is a city which combines flows of energy and resources, physical items and intellectual concepts. The online Circos tableviewer was used to generate the images.
Storage Cluster
Taking photos of inanimate objects is rewarding. Your subject doesn't complain, nor move, and a coffee break fits naturally into the workflow at any time. In this case, the inanimate object is over 3 Pb (3,000 Tb) of storage composed of a variety of Netapp appliances.
Using three gelled Hensel Integras (500 Ws monoheads — here I'm using only the modelling light for illumination along with red, blue and green filters) (lighting details), I spent some time getting to know the components up close.
See more photos.
All photos by Martin Krzywinski (Lumondo Photography).
Genesis 1.0
Our new compute cluster has been released to the user community.
This cluster consists of 420 compute nodes each with 12 cores and 48GB RAM, totaling 5,040 cores and 20TB RAM. Each node has 160GB local /tmp space and all nodes are tied together over an Inifiniband 40Gbs network.
The nodes all have access to a dedicated storage system over the Infiniband Network running GPFS with a total 700TB of usable scratch space. The filesystem is served by 8 IBM x3850 servers. All nodes are running CentOS5.4 and are using open source Grid Engine 6.2u5 as their scheduler.
Lighting details and more photos.
All photos by Martin Krzywinski (Lumondo Photography).
1 First the server room was expanded 2 It was empty and without racks, and the lights were dim. Sysadmins scurried about and unpacked equipment 3 The circuit was closed and there were electrons 4 IT staff were pleased and accounts were handed out to users 5 Who had work they called "important" 6 But which the IT staff merely called "jobs".
Photo
Periodically, I take my camera, point it at things. Here, I'll share a favourite from my creations.
This image — I will keep the subject a mystery — gives me the same feeling as some of the Hubble images. For this shot, I didn't need to reach orbit.
Other images in this series are available on flickr.
I also like geometry and lines. This shot is a tense composition of the Hancock Building at Copley Square in Boston.
and an assortment of baggage carts at St Pancreas station (London) which catches the eye.
I like to collect time in a photo, be it uniformly as in this diptych of street and traffic lights from a moving car
or blended, as in this skyline of Vancouver showing the flow of time from 5.30pm to 9.30pm.
WIZARD — Longest English Reverse Complement
DNA is composed of two strands, which are complementary. Given a sequence, its reverse complement is created by swapping A/T and G/C and writing the remapped sequence backwards (e.g. ATGC is first remapped to TACG and then reversed to GCAT).
Consider the corresponding concept applied to English words (or any language, for that matter). First, construct the complementarity map, which assigns to the nth letter of the alphabet the N-n letter, given an alphabet of N letters.
abcdefghijklmnopqrstuvwxyz |||||||||||||||||||||||||| zyxwvutsrqponmlkjihgfedcba
For example, a becomes z, b becomes y, and so on. To create a reverse complement of a word, apply this mapping and then reverse the new word (e.g. 'dog' is remapped to 'wlt' and then reversed to obtain 'tlw').
So far, that's not very exciting.
But consider the question: What is the longest English word that is a palindrome under this set of rules (reverse complementarity). In other words, it's the same forward and backward after complementing the letters. Clearly "dog" is not such a palindrome since its reverse complement is "tlw".
The answer? wizard and hovels.
wizard |||||| draziw -> 'wizard' backwards
It's an amazingly fitting answer, since a wizard is someone with special powers.
A few interesting 4-letter words that are their own reverse complement palindromes are bevy, grit, trig and wold. Common surnames that match are Ghrist, Elizarov and Prawdzik. Female first name Zola and male first name Iver are also reverse complement palindromes, as are trolig (Norwegian for 'likely', as well as an IKEA curtain product) and aviverez (2nd person plural future of 'aviver', French for 'brighten').
I've scanend a very large word list (4,138,000 unique English and foreign words) and identified 108 reverse complement palindromes. If you find a new entry longer than 6 letters, let me know.
Typefaces that are worth it
Finding just the right font is hard work. There are so many to choose from. Or are there?
If the type face is not on this list, don't use it (except Bodoni &mdash I hate Bodoni &mdash don't use it). If you need a shorter list, consult the quintissential 15 serif and 15 sans-serif fonts.
You'll notice a rotating image of type faces at the top of this page. Here's the full list.
I love Gotham and have used it in visualization projects. It's more rational than Helvetica and still enjoys a freshness that has evapourated from Helvetica after near-ubiquitous use. Don't get me wrong, there is still not enough Helvetica in the world, but more Gotham would be nice.
Paper
Anyone who has met me, quickly learns that I have a personal and antagonistic relationship with Comic Sans, the type face that shouldn't have been.
In a recent article in the journal Cognition, Fortune favours the bold (and the italicized): Effects of disfluence on educational outcomes, Diemand-Yauman et al. suggest that rendering educational materials in a hard-to-read font, and thereby recruiting the effects of the disfluency ("the subjective experience of difficulty associated with cognitive operations"), improves retention of material.
Regardless whether the effect is real, there must be better ways to improve education than through bad design.
Kittens
Surely you like kittens. So don't hurt your audience.
Side Interest Spawns Brazilian Fashion Line
In a cosmically improbable confluence of multidisciplinary pursuits, my work on keyboard layouts, which as one of its fruits has produced the TNWMLC keyboard layout — the most difficult for English typing — has been incorporated into the eponymously named Brazilian fashion line by Julia Valle.
Spatter of Network Communities
Looking into network data sets for the linear layout project, I found pretty hairballs which make a juicy spatter pattern.
I value
