Quest to Native
We have recently noticed that for some puzzles, althought the scores are significantly improved, the native is in a slightly different place then where the game community has been exploring. Currently we would like to find out of the reason why the native protein structure remains elusive in those puzzles. There are two main possibilities:
- the native structure is not reachable with current set of game tools
- we did not provide sufficient intuitiion behind the game mechanic to direct the game exploration in the direction where the native structure is hiding.
To find this out we will be posting a few Quest to Native puzzles, where the native structure will be shown as a ghost. The challenge for the community is to see if you can find the significantly better score that is around the ghost. In the process we would also be interested in whether this process gives more intuition about how native structures can pull a much higher score.
Zoran( Posted by zoran 73 1944 | Fri, 05/08/2009 - 15:23 | 18 comments )
Help Needed: Personal stories of learning through foldit
Over the course of developing foldit, it has become increasingly apparent that the game environment although always imperfect and evolving, is not only a vehicle for scientific discovery, but also for learning about proteins, and biochemistry in general.
In order to fully develop this alternate, but perhaps just as important outcome, we are writing an NIH grant to, over the next 2 years, develop an educational version of foldit to be deployed in high schools, or perhaps even middle schools worldwide. Together with learning scientists who are joining our effort, our plan is to quantitatively and qualitatively evaluate the effect of such a game on both the comprehensive understanding of biochemical underpinnings of life, but also to gauge the effect of a game like foldit on the perception that science is a cool and worth pursuing.
The grant is due this Wednesday (ugh), and we would love strengthen the proposal by including the personal stories from you about how foldit community enabled learning. So please send them in response to this blog, or email them directly to me (firstname.lastname@example.org).
Thank you.( Posted by zoran 73 1944 | Tue, 04/21/2009 - 03:22 | 1 comment )
All-Hands Update and its relation to the Grand Challenges
We have reached the final stages of our study of the effectiveness of human reasoning on the structure prediction problems. This final stage, as it turns out, will also be critical to some of our findings. Let me briefly explain what we have found so far. On well-structured localized problems foldit players do very well. On more complex problems players also do well, but it often happens that different groups or players get different parts of the protein right. Naturally, the all-hands mode becomes crucial as the key tool for combining the individual discoveries and solutions into the best solution produced by the collective "meta-brain" of foldit players. The original all-hands methodology had at least two key problems:
- the unique solutions quckly got swamped by the singular concensus solution (that is improved by an astounding amount, but still may not have contained some good parts of other solutions),
- there was no clear way to compare sectional goodness of different solutions
- there was no easy way to transfer/incorporate only the portion of the whole structure.
We have addressed these two problems in the recent release, with the following changes:
- We changed the way we cluster the candidate solutions. Now the unique well performing solutions should not be removed from the pool of good candidates. Good solutions that are very similiar to others will no longer be present.
- When viewing other solutions as ghost, their transparency and the coloring scheme points to the specific locations where the ghost solution is better, suggesting the potential partial replacements.
- with the new "copy the secondary sctructure" action you can transer portions of the proteins, and proceed with adjustments and cleanups to produce a better merged solution.
The subsequent all-hands Grand Challenges will be particularly exciting to us, and we hope that they can showcase the power of the collective mind to a much greater extent. As these challenges complete, we will be busily preparing the paper to Nature reporting the ways in which a game can do better than any currently known method for structure prediction.
foldit on NPR
this weekend a 7 minute bit on foldit airs on npr's show studio 360, and we're seeing an enormous corresponding spike of new users. Please welcome them to the "fold".
If you missed it, or don't listen to radio that much you can find the audio at the bottom of this page:
Posted by zoran 73 1944 |
Sat, 03/21/2009 - 22:25 |