Sunday, July 08, 2007

Indexing Molecules in Second Life

As I've recently commented, there has been media interest in the use of the virtual online world Second Life for chemistry. We also recently demonstrated on Drexel Island that it was possible to visualize molecular docking using the molecular rezzer developed by Andrew Lang.

Nature Island also hosts several common molecules, including buckyballs. As more people start to experiment with representing chemicals and chemistry research in Second Life it would be nice if such examples were discovered by a simple Google search.

All that really needs to be done to accomplish this is to co-locate molecular descriptors with corresponding SLURLs (Second Life URLs) on the same web page. When clicked, the SLURL will automatically start Second Life and teleport the user to the location where the molecule can be found. If the user does not have Second Life, a page pops up explaining how to set up a free account and download the software. This could be a good way to introduce the mainstream chemical community to new modalities of communicating science.

As for descriptors, I am suggesting that we use InChIs and common names at the very least. Google does a fairly good job of finding molecules by InChI.

I created a wiki,
and seeded it with a molecule from our malaria research that I've used in several places and with caffeine, which is displayed on Nature Island. I invite anyone to contribute to the wiki and add information that could be useful. (The indexing on Google can take a few days for a new wiki)

There are several other ways of creating this index and I think the more redundancy the better. For example, we could make Second Life a "supplier" on ChemSpider. It might also be possible for Andrew's molecule rezzer to note the location of a molecule when it gets created in Second Life and automatically send off an email to a Blogger account to create a post.

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At 4:44 PM, Anonymous Anonymous said...

Something else you may wish to consider doing is making them available via - that way they are geography independent of SecondLife (other than the central SLExchange repository that you use).

This in turn can take people to the molecule, where they can have it sent to them inworld with any additional information the creator wishes to provide. You can make them available for 0 Lindens (free).

I suppose this is highly dependent on how 'open' the research is considered as well - different permissions can allow different klugey forms of accepted licensing.

At 4:53 PM, Anonymous Anonymous said...

Additional thought - scripting them for ionic and covalent bonding would be very, very cool.

At 12:15 AM, Blogger Egon Willighagen said...

InChI searching via Google has actually improved: it does a quite good job too now, when one does include the InChI= prefix. I just tried it with caffeine, and excluding it, as I used to recommend doing searching in the past 1-2 years, yields 41 hits, while including it, so using the full InChI, yields 39 hits. I have not checked which ones did not show up in the second search, but that might very well be websites which excluded the prefix themselves.

So, cheers to Google for fixing InChI searching!

At 10:16 AM, Blogger Jean-Claude Bradley said...

The wiki is now indexed in Google - a search with the caffeine InChI and "slurl" pulls up the page with the location in Second Life. Also just searching "caffeine slurl" pulls it up as the third result.

At 1:49 PM, Blogger Jean-Claude Bradley said...

Taran - thanks for the suggestion. That might work well for molecules with simple names but may not for those that can only be found using a long InChI. But we'll play around with it. Our research is completely open so there are no security issues to worry about, at least for our molecules.

At 5:59 PM, Blogger Unknown said...

Maybe I'm too stupid, but the 'second life" links to the Drexel universe are telling me that the coordinates do not exist.

I just get an empty search window.


At 5:42 AM, Blogger Jean-Claude Bradley said...

I just checked the 3 slurls to Drexel Island for SLM001 and all work fine. Do you get an error when you click on those slurls or after? Do you have Second Life installed?

At 1:50 AM, Blogger Garden Wise Guy said...

Hiya, and “tag”, you’re it!

I have absolutely no background in chemistry, but I thought that I'd branch out for exactly that reason, and see if I can do some bloggic cross-pollination

Not sure if you're ever up for a blogsphere "meme," but they can be kinda fun. It’s kind of like a chain letter filled with fun personal facts. I tagged you for "8 Fun Facts" if you choose to over to…, read the rules and jump in.


Garden Wise Guy


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