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As some you may have noticed we've had a large influx of new players due to the Nature article and the following press interest. If you're a veteran Foldit player, we encourage you to help out the new players as they go through the intro levels and start working on challenge puzzles. It is exactly the community of Foldit players that makes this project so amazing.

I have also posted a blog entry explaining the source of our downtime last week, and the partial functionality we've had for several days afterward in another blog post http://fold.it/portal/node/988176
We've learned a lot from these, and we should handle future downtimes more gracefully.

Dear Foldit users,

as most of you know, we've had partial functionality of the game for a number of days. Here is some background behind what happened. Two days before the Nature paper came out, the cooling system in the machine room hosting foldit servers malfunctioned. The temperature reached the threshold when the power automatically shuts off in the entire room. This has happened before, and in the past we have recovered quickly by starting up all our servers. Unfortunately, this time the sudden loss of power completely trashed our RAID file server. Unlike our database server and the web servers, we don't have the shadow copy of the filesystem so when it went down everything went down. During that time most of the key personnel was out of town (I was in Norway, Seth in Japan, Firas in Turkey, etc), and helping remotely proved to be very challenging.

We then tried to copy all the information from the filesystem RAID disks. The second attempt of trying to copy this massive set of files worked. At that point we decided to resurrect the copy of the server on our development machine. This copy had some functionality missing, but because of the big press wave, we decided that it was better to have a partly working server than no server at all. The next day the main servers were ready at which point we switched back. As a result of all the copying, some parts of the system didn't have the right permissions set which still left some parts of the system not functional. At the same time, the database server was at it's limits for the queries it can possibly server due to the fact that we had an 80-fold increase in daily registrations due to the press wave. We've had press waves before, but we've never seen this magnitude of interest. the DB server query queue had to be restarted several times in order to not completely bog down. this of course created many in-game and web portal timeouts.

From what we can tell it seems that all the functionality is back.

we've learned several things from this perfect storm. We will use facebook as an update mechanism in the future in the case our web servers are not functional. we'll also have our development server ready to be switched as a main server with limited functionality as a temporary solution. Longer term, as soon as we get funds to revamp our server structure, I have decided to move the entire server structure to the cloud (most likely Amazon services), which will make it completely robust to failure of any individual machine. Furthermore, we can easily scale up the entire infrastructure any time we need to increase our capacity.

Our apologies to all of you who were frustrated with the lack of full functionality in the past days. It is still possible that partial of full downtimes happen, but we'll be keeping you up to date on the blog (and facebook if the whole server is down.

feel free to respond to this post if you notice some functionality still missing.

Zoran

Finally the nature paper is out. Congratulation to all Foldit players and now authors!

in addition to the journal paper, there is also a long article in Nature magazine on citizen science (featuring one of our players), and the nature also did a video (featuring two of our players). and a lot of other press ranging from New York Times to The Economist that came out concurrently with the Nature paper. Links below, and congratulations to all of you again. For those of you who cannot read the actual article (Nature journal requires subscription) let me know, and i'll send it to you provided that you are an active foldit player. We checked and this should be legit since all foldit players are authors.

UW Press release:
http://uwnews.org/article.asp?articleID=59530

Nature pages:
http://www.nature.com/nature/journal/v466/n7307/edsumm/e100805-10.html
http://www.nature.com/news/2010/100804/full/466685a.html
http://www.youtube.com/user/NatureVideoChannel

Press coverage sampling:
http://www.nytimes.com/2010/08/05/science/05protein.html
http://www.economist.com/node/16740629?story_id=16740629&fsrc=rss
http://www.pcworld.com/article/202617/fold_proteins_help_cure_diseases_i...
http://www.usnews.com/science/articles/2010/08/05/world-of-proteincraft....
http://www.theregister.co.uk/2010/08/05/foldit_victor/
http://www.wired.com/wiredscience/2010/08/crowdsourced-protein-folding/
http://www.scientificamerican.com/article.cfm?id=gaming-the-system-video...
http://cosmiclog.msnbc.msn.com/_news/2010/08/04/4814345-gamers-solve-pro...
http://blogs.discovermagazine.com/notrocketscience/2010/08/04/foldit-%E2...
http://www.sciencenews.org/view/generic/id/61809/title/World_of_proteinc...
http://arstechnica.com/science/news/2010/08/gamers-beat-algorithms-for-f...
http://www.technewsdaily.com/gamers-go-where-computers-cant-in-solving-a...

Dear folders, we are having technical difficulties with the Foldit servers. We expect to have the game and this website back up working fully later today. Sorry about the inconvenience.

For the puzzles in the CASP9 Refinement category, the CASP organizers have seen the native solved structure already and picked a submitted prediction that is closest to the native. They give us this model and tell us which regions are incorrect, making it easier to focus on which areas of the model to refine.

For 332: CASP9 Refinement Puzzle 2, they told us that "in particular two loops around residues 41 and 55 are substantially off".

In the image below, the starting model given to us is shown in black with the recently released native in blue. The loops they told us about are indicated in red (these were shown in note mode in the puzzle). The 5 other models shown in the figure were the top scoring models from the top 5 Foldit groups for puzzle 332. These models barely changed the indicated region (focusing more on the loops in the bottom left).
We did not submit these top scoring models and instead had to submit much lower scoring Foldit predictions that had refined the indicated loops.

To insure that the regions we have been told are incorrect get sufficiently refined, we are adding conditions to these areas of the protein. You score will not count until you have changed those regions (indicated in note mode) by a certain amount (shown in the conditions tab under your score).

Foldit performed very well in the refinement category at CASP8 (the TR targets in: http://fold.it/portal/node/729520) so we want to insure that you all do as well at CASP9!