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Rising to the "Science Visualization Challenge"

CmdrTaco posted more than 7 years ago | from the what-graph-charts-suck dept.

Science 30

ahab_2001 writes "The NSF and the journal Science have announced the 2007 winners of the annual Science and Engineering Visualization Challenge, mounted each year "to encourage cutting-edge efforts to visualize scientific data." There's a write-up of the winners in the journal, and also a slide presentation showcasing the winning images and videos."

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Dying field (-1, Troll)

Anonymous Coward | more than 7 years ago | (#20801461)

Visualize this: God created the earth 6000 years ago.

Re:Dying field (0, Offtopic)

Daniel Dvorkin (106857) | more than 7 years ago | (#20801751)

Visualize this: God created the earth 6000 years ago.

I can visualize that just fine; Genesis has some great imagery. I can also visualize a cow licking the first man out of a block of salt. Now, do you have some data we can throw into those visualizations? Let us know when you get some.

Moebius Transformations Revealed (4, Informative)

Anonymous Coward | more than 7 years ago | (#20801485)

Re:Moebius Transformations Revealed (1)

c_forq (924234) | more than 7 years ago | (#20801567)

The video is also embedded in the slideshow, which I would encourage people to check out as there is some amazing work showcased.

Prefuse.org visualization toolkit (3, Interesting)

Lord Satri (609291) | more than 7 years ago | (#20801599)

I've been amazed by the Prefuse.org open source visualization project [prefuse.org] and its Vizster [jheer.org] subproject. My only sadness is it's still beta.

From the site: "Prefuse supports a rich set of features for data modeling, visualization, and interaction. It provides optimized data structures for tables, graphs, and trees, a host of layout and visual encoding techniques, and support for animation, dynamic queries, integrated search, and database connectivity. Prefuse is written in Java, using the Java 2D graphics library, and is easily integrated into Java Swing applications or web applets. Prefuse is licensed under the terms of a BSD license, and can be freely used for both commercial and non-commercial purposes."

Re:Prefuse.org visualization toolkit (1)

leenks (906881) | more than 7 years ago | (#20804777)

It's a great toolkit - I think a new version is due sometime in October from what I've read on the forums.

Re:Prefuse.org visualization toolkit (1)

skeeto (1138903) | about 7 years ago | (#20807411)

A visualization toolkit? Just write some C from scratch. :-P

More seriously, I recently wrote a Mandelbrot set renderer in C. The program is geared towards running on clusters because it uses many processes to generate a single fractal or series of fractals as part of a zoom sequence. I happened to have just done a writeup about it over at my website, null program [nullprogram.com] . I have videos of some zoom sequences up there for viewing pleasure.

Re:Prefuse.org visualization toolkit (1)

kramulous (977841) | about 7 years ago | (#20808325)

Some pretty tidy work there. In case you are after some extensions (to the view ability) check out http://local.wasp.uwa.edu.au/~pbourke/projection/Wii/index.html [uwa.edu.au] . Although it uses a wii as a controller, I think the really cool thing is the "navigable movie" aspect. In your case, you could render extremely large images (yes, I know there is a limit of decoder speed and disk IO) and write a quicktime movie player (using the API) so that while the movie is playing, you can navigate around.

The link is on Paul Bourke's site, and if you are in anyway related to visualisation, you should check it out. Especially the fractal stuff (and there is a *lot*).

It's pretty and all, but ... (5, Insightful)

Daniel Dvorkin (106857) | more than 7 years ago | (#20801715)

There are times when visualization becomes an end in itself, not a tool for understanding. If what you want to do is create art from the natural world, that's great -- the showcased entries are undeniably beautiful, and I especially wouldn't mind having a the bat flight poster on my wall -- but it's a mistake to think that this is necessarily the best way to convey scientific information. There really are "two types of people in the world" when it comes to this sort of thing: call them visual learners and verbal learners, geometers and algebraists, GUI people and command-line people, what-have-you. For people in the first group, looking at a picture can often lead to great flashes of insight. For people in the second group, of which I happen to be a member, the best way to understand something is to read a well-written description or an elegantly proved theorem. Figures may be helpful, but the simpler (not necessarily the prettier) the better, and usually only as a kind of "capstone" after understanding the concept as written down.

The reason this bugs me is that in my field, bioinformatics, journal articles and textbook entries are getting glossier and more picture-laden all the time, and I don't think it's helping. Everyone who publishes any article having anything to do with microarray experiments has to include (at least one) heat map, with its pretty but useless bunch of colored dots; if they did hierarchical clustering on the results, they throw in an absurdly complex and impossible-to-interpret dendrogram attached to the side. Discussions of the biological processes under study, in both bioinformatics and classical biology, are filled with brightly colored, oversimplified illustrations that contribute more to the cost and sheer physical weight of textbooks than they do to understanding. And clearly written explanations are scarce, because so much effort has been put into the figures that there's none left over for thinking about the use of language (including math) or, hell, simple proofreading.

I'm not saying visualization isn't important; it is, and people who do it well are valuable. There are times when even I struggle to understand a paragraph, then look at the accompanying figure and get that "ah hah!" moment. Until modern computer graphics became cheap and widely available, visual learners were often left in the dust, and I'm glad that's not the case anymore. But I do think maybe the pendulum has swung a little too far in the visual direction, and for us algebraists, that's a real problem.

Re:It's pretty and all, but ... (1)

vertinox (846076) | more than 7 years ago | (#20801947)

If what you want to do is create art from the natural world, that's great -- the showcased entries are undeniably beautiful, and I especially wouldn't mind having a the bat flight poster on my wall -- but it's a mistake to think that this is necessarily the best way to convey scientific information.

It depends. Sometimes by reading a spread sheet you can get everything you need by raw numbers, but sometimes you just go "Oh... Duh! Now its obvious!" when you make a visualization of it. Its just the way the human mind works and it is different for some people.

That said, I really doubt you could show a screen shot of your numbers to a board of directors who would be more interested in a nice PowerPoint presentation/visualization that would make sense to those not in your field.

The down side is that I have actually talked with people who say "I have this visualization I want to achieve. How do I make my numbers match?" at which point I sigh and tell them they excel isn't magically preventing them fabricating data and even the data labels can be changed to whatever they want it to say. That is when I think visualization is mostly wrong. *coughs*

Re:It's pretty and all, but ... (1)

Daniel Dvorkin (106857) | more than 7 years ago | (#20802427)

Well, the purpose of this particular contest was scientific visualization -- the kind of stuff that goes into conference posters and journal articles and ultimately textbooks -- so the "PowerPoint for the board of directors" standard isn't necessarily the best one to apply. What works for a general audience isn't necessarily the same thing that works for professionals in the field, or students studying to become such. Like everyone else, I ooh and aah over pretty Hubble photos even though I know that's not how astronomers look at the sky; and astronomers probably think microarray heat maps look pretty cool too, but they don't actually lead to any biological insight.

Yes, but.. (4, Informative)

mangu (126918) | more than 7 years ago | (#20801957)

The reason this bugs me is that in my field, bioinformatics, journal articles and textbook entries are getting glossier and more picture-laden all the time, and I don't think it's helping.


I think you are right in that point, a picture may be worth a thousand words, but it doesn't necessarily transmit the needed information. I believe visualization is one of the most important tools in research, not for displaying information to others, but to understand the result and implications of our own research. I use Gnuplot [gnuplot.info] to check my results. Very often a glance at the graphic is enough to tell us something is wrong. "Hey, what's that spike over there?"


OTOH, when you need to transmit information, graphics should be carefully thought out. Unfortunately, engineers and scientists aren't graphic artists, and artists normally don't know enough about technology to create the most useful graphics.


For me, a good author in this field is Edward Tufte [edwardtufte.com] , specifically this book [edwardtufte.com] and this one [edwardtufte.com] and this one [edwardtufte.com] . In one of these, Tufte demonstrates how the cause of cholera was discovered using a street map of London and how the O-ring failure that destroyed the space shuttle Challenger was known beforehand, but was ignored because the engineers were unable to present their arguments in a clear way.

 

Re:Yes, but.. (1)

Daniel Dvorkin (106857) | more than 7 years ago | (#20802443)

Yeah, visualizing your own data while you're working with it is a good idea. And sometimes you luck into something that will be useful for your audience, as well. Honestly, though, I think it's not so much a matter of graphic design skills -- I'll reiterate what I said, that the simplest figure is usually the best, though of course this isn't always true -- as it is of separating the wheat from the chaff. There's a lot of visual chaff in journals and textbooks these days.

Re:Yes, but.. (1)

thealsir (927362) | about 7 years ago | (#20805701)

There's a lot of _textual_ chaffe in journals and textbooks these days too, mind.

Re:Yes, but.. (1)

kramulous (977841) | about 7 years ago | (#20808431)

Perhaps visualisation has been overused in some branches of science. Instead of reproducing the existing visual context, people should be pushing the 'science' of visualisation as well as the 'art'. The non-visual content tends to be stock standard as well as the visual.

On the other hand, there are those branches of science that continue to expand, fueled by the ever changing, ever enhancing, ever revealing visual representation of data (Volumetric data, I looking at you). Even that data, upon receivership being scalar in nature, may be massaged, manipulated and represented in higher dimensions.

I'm happy that you realise visualisation is useful and can play its part, but perhaps it is time for you to represent that material in a different light (pun most definately intended).

Re:Yes, but.. (1)

Assassin bug (835070) | more than 7 years ago | (#20802451)

It is amazing that it took even this long in the thread for someone to mention Tufte. Few have better summarized and understood the mix of form and function necessary for data visualization than Tufte. Especially for all the budding bioinformatics grads out there, read the above-recommended books!

Re:Yes, but.. (1, Interesting)

Anonymous Coward | more than 7 years ago | (#20802919)

It's funny: the more publications and work someone has under their belt, the lower their opinion of Tufte.

Of course everyone admires him to some extent, but the more accomplished (professional statisticians and authors of graphical papers and software packages) regard him as a crank-who-got-a-lot-of-things-right, as opposed to a genius. Just something to consider - I've not seen a whole lot of (science) work come out of anyone with breathless praise for Tufte.

Re:Yes, but.. (1)

Assassin bug (835070) | about 7 years ago | (#20812751)

Hmm. I disagree. I do not know if Tufte is a genius or not, but he does explore an area of need for folks who are actively participating in research (pub record does not necessarily equal active participation). Regarding him as a crank seems a bit harsh and flippant. I guess the same could be said for Jonas Salk or Francis Crick? Maybe I should be refreshed to know that the Political Science department of Yale would hire and keep a lucky crank on the faculty [yale.edu] ! I would not recommend his books for meditation, but they are worth reading and then moving on. And as I said, they are mostly useful to the graduate student. They are also most important if one needs to convey a lot of information to an audience with a short attention span (namely audiences at professional meetings or at Extension activities).

Re:It's pretty and all, but ... (1)

glwtta (532858) | more than 7 years ago | (#20802719)

heat map, with its pretty but useless bunch of colored dots; if they did hierarchical clustering on the results, they throw in an absurdly complex and impossible-to-interpret dendrogram attached to the side.

So heatmaps are probably a bit overused, but to say that they are completely useless and uninterpretable is a little harsh. Say you've run transcription profiling on 100 breast tumors, looking at the clustering results, any mildly trained trained scientist could see that say "there seem to be 3 major clusters, it's easy to identify the triple negative group, oh but it has a distinct sub-population that hasn't been characterized" (for example). There is no way to do this kind of analysis without these kinds of visualizations; maybe they don't belong in the final publication, but that doesn't mean the aren't indispensable. Or let's take PCA - can you understand the results of PCA without visualizing them?

It's all about dimensionality reduction; obviously nobody can just "grasp" 4,400,000 raw data points, and the results of any kind of clustering or machine learning algorithms need human interpretation - most of the time you can't just produce a list of the "important" findings, you have to show the whole process.

Personally, any dataset is a black box to me until I can "see" it in some remotely meaningful way, regardless of what the downstream analysis is going to be.

Re:It's pretty and all, but ... (1, Informative)

Anonymous Coward | more than 7 years ago | (#20804405)

Well the purty stuff has to convey something.
Check out http://tools.google.com/gapminder/ [google.com]
Rosling has some pretty interesting videos at Trendalyzers page http://www.gapminder.org/ [gapminder.org]

Re:It's pretty and all, but ... (1)

posterlogo (943853) | about 7 years ago | (#20811615)

I had entries that were finalists in both the illustration and animation categories for the Visualization Challenge a couple of years ago. My doctorate was in biology, but I also spent many a day teaching myself Cinema 4D, from scratch. I've always had an interest in 3D graphics as a hobby, but within a few months, I was making the most beautiful images of the system I was studying that I had ever seen. We regularly use these now for presentations to scientific and general audiences, and they are published in primary literature as well as textbooks. It was totally worth the effort, and I think the images have really helped a lot of people visualize what I work on. As you point out, your field, bioinformatics, is less amenable to retaining information and being visually beautiful at the same time. I respectfully suggest that that is simply your experience. For the macromolecular complexes I study, there is significant scientific value in visualizing them properly, as far as thinking about the problem and coming up with specific experiments to do.

tubgi8L (-1, Redundant)

Anonymous Coward | more than 7 years ago | (#20801801)

Dransom foVr their

Visual Diagram of Ricin (Castor Oil derivative) (1)

TaoPhoenix (980487) | more than 7 years ago | (#20802565)

This was my favorite desktop for a couple months.

http://en.wikipedia.org/wiki/Image:Ricin_structure.jpg [wikipedia.org]
http://en.wikipedia.org/wiki/Ricin [wikipedia.org]

"Idiot Translation"

"Squiggly Lines = Good" (Orange)
"Telephone Cords = Bad" (Blue)

Barley Grain= "Bad Telephone Cords without the assistance of Squiggleys"
AKA If the bad component can't get a foothold, it is mostly harmless.

b00bs! (0)

antdude (79039) | more than 7 years ago | (#20802639)

In one of the links, b00b/breasts are shown. Here's an enlarged shot [sciencemag.org] .

Those are nice - this one matters: (1)

Ralph Spoilsport (673134) | about 7 years ago | (#20804887)

Re:Those are nice - this one matters: (1)

kramulous (977841) | about 7 years ago | (#20808447)

Nice, provided you believe that 'peak-oil' is yet to come.

Re:Those are nice - this one matters: (1)

hitchhacker (122525) | about 7 years ago | (#20817921)

Take the current Total Proven Oil Reserves [cia.gov] , and the current Oil Consumption Per Day [cia.gov] for the world, and divide the former by the later. Assuming our current consumption rate, those reserves would be dry in around 42 years. The world's consumption rate has been increasing exponentially...

-metric

Inner Life of a Cell (1)

teklob (650327) | about 7 years ago | (#20806165)

I'm surprised nobody has mentioned this [youtube.com] video yet. My prof showed it to us on the first day of cell biology and it really genuinely created an interest in biology that I didn't have before. More detailed version is here: http://multimedia.mcb.harvard.edu/media.html [harvard.edu]
Really quite amazing, even if you know absolutely nothing about biology

boring (0)

Anonymous Coward | about 7 years ago | (#20808535)

Bah... who has time for boring science books and dull 3d-graphs... give me the multi million dollar movie version or the 2$ cartoon like http://www.larrygonick.com/ [larrygonick.com]
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