Circos – visualize genomes and genomic data

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Stan pointed me to a neat circular visualization tool, Circos – visualize genomes and genomic data. As the site title says, Circos is for visualizing genomic information, but the circular model strikes me a applicable to other domains. In fact, Camilo Arango in Computing Science, just defended a MSc thesis on a Course Browser design that uses a circular design to show requisites between courses. While the circular design is attractive, I wonder if it is misleading for linear information, like a text, if one wraps the text around the edge of the circle, the way TextArc does.

The Circos site has an interesting slide show on visualizing quantitative information by Martin Krzywinski that starts with Tufte and then shows different genomic visualization models leading up to Circos.

Ben Fry: The preservation of favoured traces

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Sean pointed me to a lovely visualization by Ben Fry called The Preservation Of Favoured Traces. The animated visualization shows the edits of Darwin’s The Origin Of Species edition by edition. It is a rich-prospect view of the entire work with color coded lines where changes were made. It was developed in Processing. Ben Fry says the following about the project:

We often think of scientific ideas, such as Darwin’s theory of evolution, as fixed notions that are accepted as finished. In fact, Darwin’s On the Origin of Species evolved over the course of several editions he wrote, edited, and updated during his lifetime. The first English edition was approximately 150,000 words and the sixth is a much larger 190,000 words. In the changes are refinements and shifts in ideas — whether increasing the weight of a statement, adding details, or even a change in the idea itself.

PONTYPOOL | Shut up or die

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Last night I watched a Canadian gem of a zombie movie, PONTYPOOL | Shut up or die. The movie takes place almost entirely in a radio studio in the basement of an old church in the small town of Pontypool Ontario. Grant Mazzy, a talk-radio host at the end of his career, exiled from the big city, stays on the air dealing with the eruption of a language plague where English words (primarily endearments like “honey”) carry the new type of virus that infects people. With his producer and technician they try to figure out what is real or not as strange reports come in and they are interviewed by “our affiliate” the BBC. Eventually the zombies, who follow the sound of speaking, repeating words or phrases, break in to try to eat their way to the voice. Grant and his producer figure out that talking in their poor French (remember the importance of bilingualism in Canada) is one way to avoid infection and they work out a cure which involves disrupting mean by asserting things like “kill is kiss”. Back on the radio to talk through the cure, the movie ends with a count down from 10 in French from off camera. Are the French Canadian troops sent in to eradicate the plague about to blow up the radio station just when they have figured out the cure? Was the talk show of the radio station the source of the plague in the first place or was it the posters for a lost cat “Honey” plastered all over town? Could the interview Grant gives to a BBC news announcer have spread the logorrhea abroad? Can words spread ideas (or memes) like a plague closing down our understanding until we are babbling zombies. After all, in the beginning was the word, not its understanding.

Talking of how zombie movies are often a metaphor for things we fear infection from like communism, the author of the screenplay and original book, Tony Burges, says about the movie that,

(a zombie is) really a metaphor for metaphors that keep hunting you long after they have been meaningful. They keep coming at you. … They’re figures of speech that become predatory long after their sort of meaning as figures of speech have sort of left the stage. And so … that for me is the interesting last hundred yards of a zombie’s life. (From an interview with Tony Burgess in December of 2008 at the Drake Hotel in Toronto. Interview by Ian Daffern, co-produced and edited by Tate Young of Vepo Studios.

Intensity Challenge in Humanities Computing @ the University of Alberta

Well we have started the first Intensity Challenge experiment for the Humanities Computing MA students and selected Computing Science graduate students. The idea of the challenge is that, working in teams, they have a week to to a challenge project. This year’s project is to develop an Alternate Reality Game. Next Tuesday we all gather and the teams present their games, designs, or whatever they do for this challenge. Let the team with the most points win!

The point of the challenge is to give incoming students an immediate experience of how different humanities computing is here – to orient them to doing team projects with multiple components using the resources at hand. Here is the FAQ from our instructions:

Do I have to be good at something to participate? Absolutely not, but you need to be willing to try. One of the goals of this is to help you figure out what you want to learn and how to learn with others.

Will you tell us what to do? Absolutely not! You are a graduate student. Figure out what you want to do and how to do it. At the end we will tell you how we would have done things, if you ask us. There will, however, be times when you can meet with people on campus who can help you.

I will need to go to a class during the week – is that OK? Of course, work it out with your team. Managing the time of team members with differing commitments is a real challenge, and a skill we all need to improve.

I think this is neat, but have to work during that week. Can I audit? No, this isn’t for credit so there is no such thing as auditing. You participate or you don’t. The key is how you communicate the work you have to the team. Ask a team if they will include you. It is up to them.

I have a friend who wants to do the music for this, but she isn’t a graduate student. Can others help out? Of course. Like any real project, the more you can involve the right people the better. Just don’t exploit anybody.

How much do we have to write up? That’s something you have to work out. A Design Document can take different forms, but there are faculty members with this sort of expertise. Track them down!!! We will tell you some of the things you should include, but part of the project is figuring out its scope.

What do I present at the end? Present your game. Be creative. Perhaps answer some of the questions we asked at the end of page 1. Make sure you know how to present in the HuCo lab (Old Arts 112). If you don’t know how presentations are structured, then ask around.

Does the game have to be fun? Depends on your objectives. Is it a Serious Game? Is it a “game” at all? You might want to discuss “games” with your team. Perhaps your team could answer this question with a game.

Can we cheat? Sure, if you can figure out what cheating is. That doesn’t mean we will be impressed. What you shouldn’t do is anything illegal, unethical, dangerous, or academically dishonest (don’t plagiarize.)

Is this experience a game? Not really, it is designed to give you experience running a project all the way from conception to delivery, even if incomplete. This experience will inform the more detailed discussions in the courses ahead. On the other hand, there might be some playful aspects, and we might throw in a few curves as the week progresses.

Street fighting, Earth’s calmest spot, e-mail rudeness

The Globe and Mail today (Thursday, Sept. 3rd, 2009) have an interesting tidbit on e-mail rudeness in the SOCIAL STUDIES column on Street fighting, Earth’s calmest spot, e-mail rudeness.

E-mail rudeness

Vicki Walker was forced out of her job as an accountant at a health-care company in Auckland, N.Z., after colleagues complained her e-mails were too “shouty” and confrontational. A tribunal heard that she spread disharmony among her co-workers by sending missives with entire sentences in capital letters. She also behaved “provocatively” by highlighting key phrases in bold or red, according to her employer, ProCare Health. The panel found that, while she had caused friction in her office, her conduct did not amount to grounds for dismissal. Her firm had no e-mail style guide, meaning employees could not be certain about what communications were deemed unacceptable. Ms. Walker was awarded $12,600 and plans to appeal for further compensation. (L6, by Michael Kesterton)

The New Zealand Herald has a story Emails spark woman’s sacking by Rebecca Lewis (Aug 30, 2009) with more detail including the one offensive email submitted as evidence.

Rock-afire Explosion Clip – Rockafiremovie.com

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Shannon pointed me to The Rock-afire Explosion, an animatronic band from the 80s that was one of the entertainments at Showbiz Pizza. Rock-afire Explosion has been resurrected by a fan and one of the original creators of Creative Engineering who are programming tunes and uploading video to YouTube. See, for example, Madonna’s 4 Minutes. They take bids on New Shows to Program at a strange and not very clear site. If you bid high enough and it isn’t “dirty” they will program the animatronic band to do a song you want. (Would they do Plato’s dialogues?)

I cannot begin to describe how strangely captivating this all is. Perhaps the documentary made about it (see Rockafiremovie.com) captures the passion. Or, for a computing perspective, see the clip about Programming the Rock-afire Explosion.

Whatever happened to animatronics? Will it make a comeback now that we all carry around smartphones that can control things?