Monday, October 19, 2009

Interactive 3D Visualisations of Biological Molecules Integrated into the Scholarly Literature

The embargo has now been lifted on the announcement from PLoS ONE - partially reproduced here:
On October 20th 2009, PLoS ONE will feature an impressive new 3D molecular animation technology on five newly published articles. This represents the start of a new PLoS ONE collection entitled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC” (also known as the ‘Structural Genomics Consortium’).

These peer-reviewed articles, which include some of the research highlights from the SGC, describe new protein structures, including a protein involved in the survival and proliferation of cancer cells, a protein associated with hereditary paraplegia, and a protein involved in degrading foreign compounds and pollutants in the body.

Readers of these enhanced articles will first need to download a free plug-in for their browser but will then be able to click on hyperlinked text within the article to ‘fly’ to the relevant position within the molecule, and to then interact with it at will (by zooming, rotating and exploring). The functionality, whereby the text of an academic article is tightly integrated with an animated and interactive molecular structure, provides an entirely new and enhanced experience with a significant “wow” factor.
The first enhanced articles are available here. I've been trying to evaluate these but I'm having trouble downloading the required plug-in: it is very slow and has just stalled on me. Maybe the problem is on my side so I'm asking the community to give these a spin and report. I am especially curious about the comparison with Jmol. This particular plug-in does not use Java at all from what I can glean from the press release.

Notwithstanding these probably temporary issues I think this is a very exciting development for scientific publication in the life sciences.

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At 10:44 PM, Anonymous Anonymous said...

I too am finding the download excruciatingly slow. About 10 kb/s.

Webkit nightlies now include WebGL. With this being standardized by Khronos, I imagine Firefox will also adopt this. I would consider this enough to push for some kind of javascript library to control an in-browser representation of molecules.

I'm very excited for a future that is instead plugin-free.

At 1:26 AM, Blogger Binfield said...

Try the Oxford mirror site for the plugin download.


At 9:30 AM, Blogger gilleain said...

I used the Oxford mirror, and it worked fine. The company that provides the plugin is in California, and their website is being very slow...

As for the comparison to Jmol : it's got reasonable functionality - from what I can see.

Unfortunately, there seems to be no pop-up window, so I can't access custom selections or representations. This may be deliberate, but it's annoying.

At 11:43 AM, Anonymous Anonymous said... <-- Javascript chemistry gui library based on HTML5, and the company says they will be supporting WebGL as soon as it is adopted

At 2:01 PM, Blogger Jean-Claude Bradley said...

Gilleain - when you say pop up do you mean the menu that shows up from a right click? You get the same menu by left clicking on the icon on the lower right. It does not have the same breadth of choices compared to Jmol - at least in the example I saw.

At 2:54 PM, Blogger gilleain said...

Jean-Claude: Yes, that's correct. The right-click Jmol menu has almost all the options you could need.

The left-click menu on this new browser has scenes (which is nice) but not much else.

I wanted to do things like set the label color to be white, and the background black, or vice-versa.

At 2:59 PM, Blogger Jean-Claude Bradley said...

Maybe the idea is to limit options - since this is a "published object". The authors may want to only publish specific perspectives.

At 11:45 AM, Anonymous Wen Hwa Lee said...

Check the bottom of any enhanced article (in the text frame): you can download the datapack (free) and a fully functional viewer (ICM-Browser, also Free). The ICM-Browser will allow you to do things like checking the full sequence, selecting regions in the sequence to see in the structure, different represenations, etc. And finally - extract the image with one click.



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