Balneus

Australian Lefty on Politics, Governance, Science and Info Management

Is it a bird? Is it a game? No… it’s SUPER JOURNAL!

Posted by Dave Bath on 2009-10-20


iSee/PLoS Idiot Guide

iSee/PLoS Idiot Guide

On your marks, ready, steady….. GEEK!

It’s an ultra-cool, life-like (well, if you are a radical) interactive 3D virtual world that you fly around, zoom in on details… installed as a browser plugin, but it’s not a game, it’s part of an open access, free, peer-reviewed scientific journal publishing exercise!

And promises of more and more "landscapes" coming up….

In the top-level article at PLoSOne, "Structural Biology and Human Health: Medically Relevant Proteins from the SGC" , you can find links to the hows and whys of the initiative, as well as links to the first few 3D interactive peer-reviewed "papers".

Read the installation instructions, and zoom around molecules (seeded by The Structural Genomics Consortium, that puts sequences of important molecules into the public domain so they cannot be stolen – i.e. "invented" by Big Pharma, and worked on the browser plugin.)

After the plugin is installed, choose the "enhanced" version of the scientific papers at PLoS, or go browsing around the collection at the SGC (no… not StarGate Command… much more useful).

Or get it via PLoS which might be easier, up in the paper’s abstract, you’ll see a link "enhanced version" (try this one, click that and your browser window will split with the molecule on the right (you’ve restarted your browser after installing the plugin, haven’t you) and the main text on the left.  If you haven’t got the plugin installed, you’ll be given a link to pick it up… then exit your browser and start it up again.

OK, so little John and Betty, larval internet addicts, might find this cool enough to get interested in biochemistry by flying around rather than using it seriously, but that’s fine.

When will journals (or government agencies) in other disciplines start doing something just as cool and informative?  Particle physics?  Mathematics?  Astronomy?  Economics?  Sociology?

Personally, though, I’d like to see you be able to swap something and watch the conformational changes, Hbβ 6 Glu->Val for instance, and able to control the pH and amount of water around the thing… but that’ll come.

Well, whadaryawaitinfor?  Oh, that’s right, the download servers are probably being hit very hard!

Anyway, here are a couple of shots of the same paper, the same dataset, before choosing a different rendering method and a bit of zooming and rotating (click for bigger versions).

Looking at a molecule one way, just before changing to a different way of looking at it

Looking at a molecule one way, just before changing to a different way of looking at it


The same molecule after selecting another rendering, then rotating and zooming a bit

The same molecule after selecting another rendering, then rotating and zooming a bit

A third way of looking at the molecule

A third way of looking at the molecule

A fourth way .... almost the same position as the third

A fourth way .... almost the same position as the third

Another, same rendering method as before, but zoomed in and rotated to see EXACTLY how the ATP fits into gaps in the proteins and gripped for splitting

Another, same rendering method as before, but zoomed in and rotated to see EXACTLY how the ATP fits into gaps in the proteins and gripped for splitting



UPDATE:  This video displays some of the interactive features, is from the post on scienceblogs/everyONE and includes mention of early reactions to the PLoS enhancements, and ahem, guess who seems to have been first off the mark?

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One Response to “Is it a bird? Is it a game? No… it’s SUPER JOURNAL!”

  1. […] the explanation on everyONE blog and the first reactions by Dave Bath, Jean-Claude Bradley and Nick […]

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