Molecules and supercomputers in Second Life

It is strange as we talk about this project all the time, yet as Ugotrade was looking for a link to it on eightbar it turns out we had not covered it well enought. So here we go.
We have said before about taking things from one place and regerenating them in another to find interesting ways to visualize data and system architectures and workflows in a business.
This project by our collegues in Watson took the result of some complex protein folding on a blue gene supercomputer and then injected the result of those calculations on the structure of a rhodopsin molecule into a scripted object in Second Life which then built a huge representation of that molecule.
The guys have an interview here over on Rez Tone and Zha Ewry are the main contacts.
The interesting thing is that as well as being a scientific visualization it has a place as an art installation and a though provoking place to gather. Inventiably when people gather there they tend to ask so what is this then? This leads to much deeper conversations about life sciences and supercomputing at IBM.
I tend to use this little clip of me sitting in the molecule to deomstrate the scale of this. Remember its all generated, not a manual build.

9 thoughts on “Molecules and supercomputers in Second Life

  1. There is actually quite a lot of molecule rezzing going on in SL, albeit on a smaller scale than rhodopsin (you might want to fix that link btw). You can rez a peptide live on IBM Almaden and there is even an SL Molecular Structure Group (which includes an IBM av) due to have its first meeting later this month. There is a fledgling database of structure availability/deployment hosted off the wiki at as well as a script that does a little of the parsing from pdb files. As a personal project I’m hoping to produce a toolkit that makes this kind of build more accessible to teachers and students. We had an informal meeting on ANGEL just before Christmas which I recorded on my blog ( It was just great seeing those structures rez! (SL: Graham Mills)

  2. Pingback: UgoTrade » Blog Archive » “Exploring Reality in Virtual Worlds” with Piet Hut

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  4. There is obviously a lot to know about this. I think you made some good points in Features also.

  5. I just have to post about this, but this reminded me of the just released news with Craigslist’s CEO demanding for an apology from the AG of South Carolina. Always something new with Craigslist and things in the news.

  6. found your site on today and really liked it.. i bookmarked it and will be back to check it out some more later ..

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