Saturday, February 07, 2009

NMR game on Second Life

Andrew Lang and I have been discussing publishing our work on chemistry and Second Life. We're working on the draft here. When going over the game section, it became clear that we'll probably need to make two manuscripts out of this. This is an opportunity to wrap up my previous work on the EduFrag project - using Unreal Tournament to teach organic chemistry. I had submitted that article but as it was going through the peer-review process the approach was essentially made obsolete when we adapted the quizzes to Second Life.

So Andy and I brainstormed some new chemistry games that we could introduce to Second Life to leverage our recent tools. One of the applications is the NMR game. By combining the orac molecule rezzer, the SL spectral viewing tool and ChemSpider Open Data spectra I think we have a pretty good game.

The idea simple: click on the molecule that is represented by the spectrum. If it is correct you get 2 points and get another spectrum. You lose a point by clicking on an incorrect molecule. After going through all the spectra your score gets posted on the web to a top10 list. For equal scores the best time takes it.

From an educational perspective this is useful I think on several levels.

First the ability to look at the molecule in 3D makes it easier in many cases to demonstrate the relationship between Hs, which is critical in NMR.

Second we are using real spectra - not simulations. That is a great opportunity to teach students about how to deal with impurities, solvent peaks or quirks in the peaks. The viewer allows for easy zooming by typing commands like "zoom 1.5-2.5" in the chat box.

Third this spectrum viewer uses Open Source JCAMP-DX files so it can (and will) be adapted to all kinds of spectra - like IR, UV, MS, C NMR, etc. I'm teaching (CHEM 242) all of those techniques this term so I'll have an opportunity to see how well it works.

There is currently a copy of the game on ACS island (SLURL) - give it a try and give us some feedback.

Here is picture of the game area (Viv is sitting on the molecule and I'm on the spectrum):


At 9:59 AM, Blogger Egon Willighagen said...

Brilliant! I think I am going to have to get SL installed again :)

At 10:06 AM, Blogger Jean-Claude Bradley said...

Great - let me know if you run into any problems trying the game.

At 11:40 AM, Blogger Unknown said...

I'm out trying to resource additional spectral data for the game!

At 12:14 PM, Blogger Jean-Claude Bradley said...

thanks Tony!

At 11:14 AM, Blogger gilleain said...

Hi - Great idea, but the implementation could do with some improvement :)

On the grounds that you shouldn't criticize unless you have some ideas, here are problems:

1) I tried it for C-NMR. You can simply count the peaks, and compare to the number of carbons in the structure, right?

2) You can get the same structure more than once in the candidate list.

3) This game doesn't have a learning curve so much as a learning cliff.

Ok, so some possible solutions:

1) Only use structures with the same number of atoms.

2) Check for duplicates.

3) A tutorial? Some kind of limited peak picking/selection interaction with the molecules?

If you need software, I am a CDK developer, and would be happy to give help, if you wanted it.

Did you see the foldit game? That was a large development effort, so it's not a fair comparison at all. However, what is interesting about it is the number of non-expert users who were drawn in.

I mean really really non-expert - like calling alpha-helices "curly fries" :) Maybe folding is quite a visual thing that many could do, but I do think that it's a worthwhile goal to have...

Lastly, thankyou for making this game - maybe I can actually learn something about spectra...

At 12:15 PM, Blogger Jean-Claude Bradley said...

There is a link to a YouTube tutorial on the front page of the web version of the game. If you're asking about a tutorial on how to interpret spectra I don't think there are any shortcuts. This is intended for students who are learning or have learned NMR in their classes.

Yes the C NMR can be figured out easily if the structures have different numbers of carbons. We could probably do something about that.

If you find any duplicates or problems with the spectra please use the link in the game to flag and make a comment. You should not be getting duplicates.

Thanks for offering to help with your CDK experience! If there is a component that you would like to build lets definitely discuss.

At 1:21 PM, Blogger gilleain said...

Ah, yes actually I did watch the youtube tutorial. That is good. However, I mean that it would be possible to teach students spectroscopy through the game - levels of difficulty, for example by increasing the number of candidates.

Also, less of the 'sudden death' nethack-style could be more encouraging :)

To be clear, I meant duplicates of the molecules, not duplicate spectra.

As for software components, well I should ask - what molecule drawing code are you using? (and did you see the javascript molecular editor recently made?).

I could imagine that an integrated spectrum/molecule applet could allow the player to assign peaks to aid the identification of the correct candidate.

At 1:42 PM, Blogger ChemSpiderman said...

Some updates re data: Another 30 H1 spectra provided today from my alma mater. These are drug like compounds.

Gilleain..lots of ideas here and I will connect offline with thoughts but basically:
1) Can the NMRShiftDB be exported in JCAMP format as synthetic spectra so that we can load onto ChemSPider and view in JSpecView OR should we just deliver them as "synthetic spectra" through the NMRShiftDB applet?
2) Some examples of the "same structure" would definitely be useful to debug
3) For C13 our webservice can be used to find structures with the same number of carbon atoms. Also, eventually, to find "similar structures"
4) Please point me to the JS molecular editor...send me an email is fine
5) yes to an integrated applet/molecular editor...can it be done with JSPecView as the base viewer so that there isn't yet anther applet....

At 6:30 AM, Anonymous Anonymous said...

Nice game !

The reality can be found on

Wolfgang Robien

At 4:05 PM, Blogger Yttrai said...

I would love to try this, but currently the spectrum only shows an image of a cat, and will not allow itself to be reset.

Are you still supporting this? Can you look into the issue?

(I opened all the links and none led to plug ins, though if that is the issue either the plug ins have been moved or are not obvious from the links.)

Thank you!

At 4:45 PM, Blogger Jean-Claude Bradley said...

If you see a cat you need to click on the media play button in Second Life. The game in Second Life should work but does not have many spectra. Check out the web version with over 1000 spectra:


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