Messages from Prof. Vijay Pande

[Saryn]

I wondered why almost every Uniprocessor WU was about the Abeta peptide. Glad to see my processing helping out :D

[Blacksmith1]

good to see some results. makes me feel like I'm not just wasting electricity.

[Saryn]

good to see some results. makes me feel like I'm not just wasting electricity.

Exactly. I know results can take months or years to come out, but it would be nice to see more updates to let us know something IS being done.

[Leganfuh]

Folding@home

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu

(c) 2007 Vijay Pande


August 10, 2011

2012 Michael and Kate Bárány Award

I have some good news. Due in large part to the work we've done with Folding@home, I've been named the recipient of the 2012 Michael and Kate Bárány Award for Young Investigators from the Biophysical Society for "developing field-defining and field-changing computational methods to produce leading theoretical models for protein and RNA folding." This was just annouced in the Biophysics Society newsletter and their web site hasn't been updated just yet for the 2012 awards.
As with all of the accolades coming to our work, this is very much a team effort, and I'm excited that our collective work is being well-recognized.

[Blacksmith1]

I filmed a new interview about Folding@home, which gives some potentially interesting details about FAH especially for those who are new to the project.
The show is Futures in Biotech 85: Modeling Life With The World's Most Powerful Computer System. Dr. Vijay Pande, Stanford's Director of Folding@home, details how the World's most powerful system models Alzheimer's and other human diseases.

go check it out.

[Blacksmith1]

Two recent blogs from Dr. Pandeone is about an Update to the V7 client.

October 11, 2011 Update on the v7 client – v7.1.38 is now released We've released the latest v7 client (7.1.3 8 ) in our forum. I've pasted the update from Joseph Coffland (lead programmer), outlining the progress so far.

For those running the V7 or those interested;
http://folding.typepad.com/news/2011...-released.html

The other Discuses How The Folding@Home supercomputer (yes, we qualify when all put together), and a very impressive special purpose computer from DE Shaw Researched, called ANTON compare.

October 13, 2011 Comparison between FAH and Anton's approaches Right now, the two most powerful supercomputers for studying protein folding are Folding@home and a very impressive special purpose computer from DE Shaw Researched, called ANTON. We're often been asked "how do they compare?" The approaches are very different, so comparisons aren't completely straightforward. ANTON takes the traditional approach to studying protein folding, where one performs a few (often 1 or 2) long trajectories to study the process. Folding@home takes a statistical approach, which has two primary benefits: 1) it can access folding on dramatically longer timescales (milliseconds, instead of microsecond folding events over a single long trajectory) and 2) it can give statistically significant results on those long timescales.

http://folding.typepad.com/news/2011...pproaches.html
Some interesting stuff for those who like info on the F@H program

[thebluebumblebee]

Planned changes to "Big Advanced" (BA) projects, effective January 16, 2012

Big Advanced (BA) is an experimental type of Folding@home WUs intended for the most powerful machines in FAH. However, as time goes on, technology advances, and the characteristics associated with the most powerful machines changes. Due to these advances in hardware capabilities, we will need to periodically change the BA minimum requirements. Thus, we are shortening the deadlines of the BA projects. As a result, assignments will have a 16 core minimum. To give donors some advance warning, we are announcing this now, but the change will take place in 2 months: no earlier than on Monday January 16, 2012.

We understand that any changes to how FAH works is a disruption for donors, and we have been trying to minimize such changes. For that reason, we are not changing the points system at this time.
However, we want to emphasize that the BA program is experimental and that donorsshould expect changes in the future, potentially without a lot of notice (although we will try our best to give as much notice as we can). In particular, as hardware evolves, it is expected that we will need to change the nature of the BA WUs again in the future.

This will rock some boats. If you are running a 4 core, 8 threaded -bigadv machine, it will become a SMP machine Jan. 16th. Even the hex core/12 threaded machine might not work for -bigadv. Angry thread at F@H: http://foldingforum.org/viewtopic.php?f=16&t=20036

[slugbug]

Well that sucks the big one 16 physical cores so server machines only. It just goes to show how little they appreciate their volunteers. I can see a lot of people quitting CPU folding altogether now.

[bumbleblee]

Well that sucks the big one 16 physical cores so server machines only. It just goes to show how little they appreciate their volunteers. I can see a lot of people quitting CPU folding altogether now.

Why exactly do people fold? For the points? It doesn't change the fact that you're still helping. I'm confused why this would really matter?

[thebluebumblebee]

Why exactly do people fold? For the points? It doesn't change the fact that you're still helping. I'm confused why this would really matter?

Points equal how much you're helping. So if a person says "I want to help this much"/ "I want to get this many points", and they spend the money to attain that goal, they will likely become less than happy, to say the least, when the investment that they've made no longer reaches that goal. No one likes to be yanked around like a dog on a leash. Someone I know built 4 -bigadv systems that got 30-32k PPD. Then the bonus was reduced and now there will be no bonus. He's quitting.

[ET3D]

The point system is quite screwed up anyway. It feels like a game, not something representative of the effort. For one thing, the passkey thing makes a huge difference, and is completely unrelated to the effort made. Another thing is that if you're not folding 24/7 when you stop folding and how much can have a serious effect on the points. Doing one unit quickly and then doing nothing for a week can give more points than doing four units more slowly during that week.

[Joshua_Mahr]

It is for the cause. Not for the points. If someone built 4 machines for folding and thats it? Why? There is no guarantee on the points system. I have many folding rigs but do you think that is their only purpose, sorry no. I must applaud those who build the rigs for just folding but you should already know the risks.

[ET3D]

A lot of time it is for the points. It's competition between teams and between people on the team. Even here you get more of a chance to win if you have more points, although luckily it's toned down these days. But it's the same elsewhere. It's a competition for many people.

[slugbug]

I'm sure if Mike was still folding he would have been very upset to hear this news.

[Blacksmith1]

Scott does that to encourage people to fold more during the contests. yes it's a bit of e-penis with the points thing, but i have been folding as much as i can with whatever I can for a long time now. stated on a simple cpu client, then learned my CPU could run the SMP. then added GPU clients. now I'm folding on 3 fermis but even if I still had my 2 9600 gso's in my sys I'd be folding just to fold. I use the points to gage how well my sys works fo folding, and a bit to play with some of our team members ( passed slug for a brief window last week) As most of you know I am no longer eligible for any of the contests. So why do I fold? Because my mom died from cancer, because people die from it everyday, because Stephanie is still fighting it, because I can. and there is nothing else I can do to help fight this thing. So if someone is only in it for the glory, then let them quit, someone else will come along and fold just because.