Messages from Prof. Vijay Pande [Archive]

Leganfuh

10-01-2010, 09:01 PM

Happy 10th Folding@home (http://foldingforum.org/viewtopic.php?f=24&t=16160#p160549)

http://foldingforum.org/styles/prosilver/imageset/icon_post_target_unread.gif (http://foldingforum.org/viewtopic.php?p=160549#p160549)by VijayPande (http://foldingforum.org/memberlist.php?mode=viewprofile&u=11) » Fri Oct 01, 2010 6:35 am
It’s with great pleasure that I announce that today is Folding@home’s official tenth anniversary. It’s been an amazing 10 years, especially in terms of what we’ve collectively been able to do, and my team and I are grateful for all the contributions by millions of people that has made this possible. If you’re curious to see what we’ve done so far, please check out our Results section or Diseases FAQ. In particular, we're very excited about recent work on protein folding, which could radically reshape how people think about folding (leading to recent awards).

Behind the scenes, we’ve been planning some 10 year celebration activities, including a new client, better client software feedback of what’s going on, some new client surprises through new collaborations, new backend software, and enhanced science via new cores. We’re also pushing to support more hardware, such as new support for OpenCL on ATI hardware (an ATI OpenMM/OpenCL core16 is in internal testing, although it requires the v7 client).

One key big picture goal for this year is our push to try to make FAH much easier, interesting, and fun to use by donors. With a new server backend soon to be in place, we should be ready to scale to much higher levels and we’re excited about what we can do with the combination of a new client that’s easier to run, much more stable backend, and new science in cores A3, A4, 15, and 16.

Finally, amongst some of the surprises are new initiatives that I hope will change how people think about distributed computing. That’s clearly a lot to hope for, but that’s our goal. Sorry for being so coy about this now, but I wanted to let people know there’s a lot going on behind the scenes and we’ll be talking about this more as we announce these initiatives throughout the year.

http://folding.typepad.com/news/2010/10 ... rsary.html (http://folding.typepad.com/news/2010/10/foldinghome-10th-anniversary.html)

:keepfolding:

Leganfuh

10-13-2010, 06:00 PM

Folding@home
A blog all about Folding@home, from its Director, Prof. Vijay Pande
Folding@home - Main
(c) 2007 Vijay Pande

October 13, 2010

Recent talk of results from Folding@home

Donors are often curious to hear about recent results. While one can read our papers, listed on our web site, those are fairly technical and intended for a biological or biophysical audience. The talk I gave at GTC 2010 ("Folding@home: Petaflops on the cheap today, exaflops soon?") was intended for a computational audience, so it may be more approachable than the papers, especially for those more familiar with the computational side of FAH, rather than the biological. You can see it here.

I talk a bit about how FAH works and some recent results in protein folding (pushing past the millisecond timescale), protein misfolding disease (Alzheimer's) and viral infection. If you're curious about how FAH works or what we've done recently, this might be of interest to you.

http://nvidia.fullviewmedia.com/gtc2010/0923-b-2007.html

Scott

10-14-2010, 02:20 PM

Good reading. Thanks for the info.

Leganfuh

11-09-2010, 12:27 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

November 08, 2010

Update in FAH stats by Operating System (http://folding.typepad.com/news/2010/11/update-in-fah-stats-by-operating-system.html)

We have been tracking down a bug in our stats by operating system page (http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats) and it looks like we have now found it. Basically, we were counting SMP clients as giving 1 CPU. This grossly undercounted the total number of CPUs, especially for Linux and OSX. Please note that we have only updated this particular page (stats by operating system) and are looking into updating other ones with the additional information of the number of CPUs per client.
For those who are curious, here's the latest as of 5 min ago:

Client statistics by OS

OS Type Native TFLOPS* (http://folding.stanford.edu/English/FAQ-flops) x86 TFLOPS* (http://folding.stanford.edu/English/FAQ-flops) Active CPUs Total CPUs
Windows 303 303 291382 3508526
Mac OS X/PowerPC 4 4 4505 141460
Mac OS X/Intel 101 101 24526 134420
Linux 295 295 109289 539508
ATI GPU (http://folding.stanford.edu/FAQ-ATI2) 896 945 6307 139443
NVIDIA GPU (http://folding.stanford.edu/FAQ-NVIDIA) 329 694 2068 215909
PLAYSTATION®3 (http://folding.stanford.edu/FAQ-PS3) 800 1688 28360 1034788 Total 2728 4030 449343 5714054

Total number of non-Anonymous donators = 1478538 Last updated at Mon, 08 Nov 2010 15:27:38 DB date 2010-11-08 16:38:48 Active CPUS are defined as those which have returned WUs within 50 days. Active GPUs are defined as those which have returned WUs within 10 days (due to the shorter deadlines on GPU WUs). Active PS3's are defined as those which have returned WUs within 15 days. *TFLOPS is the actual teraflops from the software cores, not the peak values from CPU/GPU/PS3 specs. Please see our main FAQ (http://folding.stanford.edu/FAQ), FLOPS FAQ (http://folding.stanford.edu/English/FAQ-flops), PS3 FAQ (http://folding.stanford.edu/FAQ-PS3),NVIDIA GPU FAQ (http://folding.stanford.edu/FAQ-NVIDIA), or ATI GPU FAQ (http://folding.stanford.edu/FAQ-ATI2) for more details on specific platforms.

Leganfuh

11-23-2010, 05:15 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

November 22, 2010

2 new results from FAH (http://folding.typepad.com/news/2010/11/2-new-results-from-fah.html)

Two new papers from FAH have just come out, both from the lab of FAH affiliate Eric Sorin. For more information, check out papers #76 and #77 on our results page (http://folding.stanford.edu/English/Papers).

Leganfuh

12-09-2010, 12:07 AM

Folding@home (http://folding.typepad.com/news/)

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

(c) 2007 Vijay Pande

December 08, 2010

server room maintenance: December 16, 2010 (http://folding.typepad.com/news/2010/12/server-room-maintenance-december-16-2010.html)

One of our main server rooms will be undergoing maintenance on December 16, 2010. This will mean some of the FAH servers will be off line on that day. It looks like most of the key FAH infrastructure will be up, but there will likely be WU shortages on that day since a large fraction of machines will be down.
We are working to optimize what we can by distributing jobs to servers in other server rooms, but we wanted to give donors a heads up in advance so they know this is coming.

Blacksmith1

12-09-2010, 12:51 AM

thanks for the notice. hopefuly everyone will read this, and not freak out that day. Me? I'm gonna plan a marathon game session if I don't get any WU's.

Leganfuh

12-10-2010, 10:57 PM

Stanford network upgrades – Dec 18 through Jan 2 (http://folding.typepad.com/news/2010/12/stanford-network-upgrades-dec-18-through-jan-2.html)

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

December 10, 2010

During Stanford's Winter Closure (December 18 through January 2), IT Services plans to schedule a network backbone maintenance window every morning from 4:00 a.m.- 8:00 a.m. to implement improvements in the network, as we did last year. In most cases, the changes should not affect the connectivity of departmental or home networks. In cases where they might, any interruption in service should be under 5 minutes.

While Folding@home will be up for this period, there may be brief (~5 min) network interruptions for network traffic from/to off-campus during the daily maintenance windows of 4:00 to 8:00 am pacific time. The upshot is that the campus should get improved network performance after the upgrades.

Leganfuh

12-15-2010, 09:17 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

December 15, 2010

reminder & update: server room maintenance: December 16, 2010 (http://folding.typepad.com/news/2010/12/reminder-update-server-room-maintenance-december-16-2010.html)

We've been working to try to minimize the effect of the server room maintenance coming up tomorrow. Since this is our main room, FAH will be stretched pretty thin during the outage and we expect there will be WU shortages. Also, clients will not be able to send WUs back to servers that will be unavailable during the outage.
However, some good news is that we have been able to get power to a few key machines so the stats and web page should be up as well as most of the key servers. If you have trouble getting or returning WUs tomorrow, please just wait it out until we get a chance to get everything back on line.

Scott

12-16-2010, 02:30 AM

Yeah lots of problems today getting work units for GPU3 and sending them in already. Really kind of bumming since just setting up the the 570 and 580 in one box. My main rig alone should get almost 30K points a day with the 2 GPU's.

Leganfuh

12-16-2010, 04:04 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

December 15, 2010

update 2: server room maintenance: December 16, 2010 (http://folding.typepad.com/news/2010/12/update-2-server-room-maintenance-december-16-2010.html)

It looks like we will have to take a few machines down early in anticipation of the server room outage tomorrow. Right now, it looks to be just vspg11 and vspg12 (and their related VM's). We're working to keep as much up as we can though during the outage

Leganfuh

12-16-2010, 06:15 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

December 16, 2010

update 3: server room maintenance: now (December 16, 2010) (http://folding.typepad.com/news/2010/12/update-3-server-room-maintenance-now-december-16-2010.html)

We've started dealing with all of the outage. It looks like we should have the basics online (stats, fah-web, main AS, most of the key servers), but most of the redundant systems will be down, so there could be outages even with all we've done to try to have the basics up. Hopefully this will be straightened out by the end of the day pacific time.

Leganfuh

12-17-2010, 02:27 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

December 16, 2010

update 4: server room maintenance: December 16, 2010 (http://folding.typepad.com/news/2010/12/update-4-server-room-maintenance-december-16-2010.html)

Looks like the server room updates have been completed and our team is starting to bring the servers back up. It will likely take a few hours for some, since this is an opportunistic time for some routine server maintenance (since they machines had to go down anyway). Some of the down servers are already back up and serving, more on the way in the next few hours.

Scott

12-17-2010, 12:10 PM

Good, nice to start getting work units again.

Leganfuh

12-20-2010, 06:07 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

December 19, 2010Updates thread (http://folding.typepad.com/news/2010/12/updates-thread.html)

For some time, we've been keeping an updates thread (http://foldingforum.org/viewtopic.php?f=24&t=14714&start=60) with information for every change that we do to the FAH backend (new WUs, servers on- and off-line, etc). However, many donors likely don't know about it, so here's a reminder:
http://foldingforum.org/viewtopic.php?f=24&t=14714&start=60

slugbug

12-20-2010, 06:22 AM

I didn't notice any interruptions on my end at all.

swmeek

12-20-2010, 03:43 PM

me neither!

Leganfuh

01-27-2011, 06:12 AM

Folding@home
A blog all about Folding@home, from its Director, Prof. Vijay Pande
Folding@home - Main (http://folding.stanford.edu)
(c) 2007 Vijay Pande

January 26, 2011

New GPU3 (version 6.41) client released

The latest GPU3 client is now on our high performance client download page. This new client improves GPU identification and has several other minor improvements.

For those who are unfamiliar with the other FAH clients: there are several types of high performance clients. SMP refers to multi-core GPUs. GPU3 refers to the latest generation Folding@home GPU client. Currently, GPU3 is only available for NVIDIA GPUs, but we are working on a GPU3 release for ATI. For NVIDIA GPUs, we recommend GPU3. For ATI, we suggest GPU2 until GPU3 has passed through its QA testing (going on now). Finally, the v7 Folding@home client (currently in alpha testing) has these functions (SMP and GPU) built in and will not require a special client.

jellyrole

01-28-2011, 09:40 PM

It'll be nice to have GPU3 ATI support, that's for sure!

Blacksmith1

03-01-2011, 03:43 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

February 20, 2011

Integration with Facebook (http://folding.typepad.com/news/2011/02/integration-with-facebook.html)

In preparation for our v7 client launch, we will be adding some facebook elements to our Folding@home web pages, including the http://folding.stanford.edu information page as well as stats pages. Today, we have turned on facebook links on the team stat pages, so you can easily recommend your team on facebook. While the integration will start small, we will be working to enhance it as time goes on.

Leganfuh

03-01-2011, 06:05 AM

My bad, I'm sorry.

Blacksmith1

03-01-2011, 07:08 PM

no problem. since you showed up, we'll skip the court-martial.;-)

Leganfuh

03-02-2011, 03:56 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

March 01, 2011

Introduction of a new SMP core, changes to bigadv (http://folding.typepad.com/news/2011/03/introduction-of-a-new-smp-core-changes-to-bigadv.html)

We have recently launched a new core type for bigadv work units. We're forking A5 off from our A3 core to make a core that specializes in bigadv workunits. In particular, new A3 and A4 cores use more RAM per thread which makes large-memory calculations very memory inefficient in those cores. A5 does not have this issue and looks to be a good general fix for big RAM (eg bigadv) calculations.

However, to be able to use the new A5 core, one needs to use an updated client: 6.34 or later.

We are shutting down A3 bigadv in the next day, so please update your clients if you wish to continue running bigadv work units (to be clear, all issued A3 bigadv work units will be accepted until their deadlines. We are terminating new bigadv work unit assigns). Older clients will be redirected to standard A3 SMP work units; the switchover will allow us to push an update to the standard A3 core and release a large number of new A3 work units that have been in early testing.

The SMP clients version 6.34 binaries are now posted on the high-performance download page:

http://folding.stanford.edu/English/DownloadWinOther

They can be dropped into a working FAH installation, but it's always safest to update between work units.

There are several small changes involved, but especially support for new SMP2 cores (A5) that will be released in the near future.

P.S. Do not forget the augments when reconfiguring your client.

Leganfuh

03-12-2011, 06:38 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

March 11, 2011

Testing Quick Return Bonus (QRB) with classic WUs (http://folding.typepad.com/news/2011/03/testing-quick-return-bonus-qrb-with-classic-wus.html)

We have had for some time a Quick Return Bonus (QRB) for multi-core/SMP WU's. The nature of QRB is that donors get extra points for returning the WU early. The rationale here is to align what's best to accelerate the science (getting WUs back quicker so next generation WUs can be made and sent out to donors) with what the donors see (points). In the past, we've simply mentioned to donors that it's ideal for us to get WUs back faster, but the QRB formalizes this and is an attempt to align incentives.
We are testing it with the classic A4 core now. I stress the word testing since we are looking to see what are the implications of rolling this out more broadly (there can always been unforseen complications of anything as complex as FAH). However, the general idea of aligning incentives is pretty clear, so hopefully we will be able to tweak the QRB plan if problems arise.
For more details on which project, etc, please see this thread (http://foldingforum.org/viewtopic.php?f=24&t=17841)in the FoldingForum.

Blacksmith1

03-13-2011, 05:28 PM

cool. this should give those with older, weaker systems a chance to catch up a bit.

Leganfuh

03-15-2011, 03:05 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

March 14, 2011

Progress to the v7 client release (http://folding.typepad.com/news/2011/03/progress-to-the-v7-client-release.html)

(http://folding.typepad.com/)

Leganfuh

03-15-2011, 10:17 PM

Folding@home
A blog all about Folding@home, from its Director, Prof. Vijay Pande
Folding@home - Main (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

March 15, 2011

FAH Support for ATI GPUs

We have been working to improve our support for AMD/ATI GPUs. AMD/ATI originally supported the Brook language for GPU programming, but has since moved to OpenCL, dropping support for Brook. This means that in order for FAH to support ATI GPUs, we have had to rewrite our ATI GPU core in OpenCL. This has been a huge undertaking, but is coming to fruition (check out http://simtk.org/home/openmm for details and a change log with progress updates). Due to ATI's decision to drop Brook in lieu of OpenCL, new FAH ATI GPU core development can only be done in OpenCL and thus can only run on GPUs which ATI supports with OpenCL.

We want to give ATI donors a heads up that ATI does not support all of its GPUs with OpenCL (the series 3xxx are not supported and the series 4xxx does not have sufficient OpenCL support for efficient FAH calculations). For the short term, we will support both the older (Brook coded) ATI core 11, and the newer (OpenCL coded) ATI core 16, but we cannot support the Brook-based core for much longer. We plan to support ATI core 11 until September 1, 2011 (hopefully longer, but we want to get this on donors' radars). Closing support for a given platform is never a popular decision, but in this case, we have no choice due to the lack of vendor support of that platform.

The good news is that ATI's support for OpenCL is very strong and we're excited about our new ATI openCL core (core 16), which is undergoing testing right now. ATI core 16 will be publicly released after the v7 client is released, as the core needs the new client

James86

03-15-2011, 11:54 PM

that's good and bad all the ATI cards I have are 4k series

Leganfuh

03-18-2011, 04:49 PM

Folding@home
A blog all about Folding@home, from its Director, Prof. Vijay Pande
Folding@home - Main (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

March 17, 2011

Some classic clients not being assigned (http://folding.typepad.com/news/2011/03/some-classic-clients-not-being-assigned.html)

There is a problem with the assignment of WUs to some classic clients. We are working on it.
UPDATE: Looks like the worst is over, but we are keeping an eye on this issue. In particular, the port 80 AS (assign2.stanford.edu) seems to be still having issues.

Leganfuh

03-18-2011, 09:51 PM

Folding@home
A blog all about Folding@home, from its Director, Prof. Vijay Pande
Folding@home - Main (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

March 18, 2011

WS Down: VSP07*, VSP17, VSP22 (http://folding.typepad.com/news/2011/03/ws-down-vsp07-vsp17-vsp22.html)

There is one physical box down, which means that several WS virtual interfaces are down. Our sysadmins are working on it and have given us a 6 hour ETA for it coming back up.

Posted at 10:38 AM |

UPDATE 8pm pacific time Fri Mar 18: The server is still going through its RAID arrays (it has many of them and they are very large). Our admins think this will require several more hours, putting the ETA at Saturday assuming all goes well.

UPDATE 5:30am pacific time Sat Mar 19: The server came up an hour ago and looks to be running ok now

Leganfuh

03-29-2011, 09:00 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

March 29, 2011

Planned server outage: tomorrow, Wed Mar 30 from 10am to noon pacific time (http://folding.typepad.com/news/2011/03/planned-server-outage-tomorrow-wed-mar-30-from-10am-to-noon-pacific-time.html)

We have a planned outage tomorrow, Wednesday March 30 from 10am to noon pacific time. The stats update and fah-web.stanford.edu web pages will be down, but FAH will be running otherwise. Stats will still be accumulated by the Work Servers, just not related to the web page until those servers go up.
So, other than seeing stats updates, everything should look normal for FAH during the outage.

Posted at 09:39 AM | Permalink (http://folding.typepad.com/news/2011/03/planned-server-outage-tomorrow-wed-mar-30-from-10am-to-noon-pacific-time.html)

Client version 7 now in open beta (http://folding.typepad.com/news/2011/03/client-version-7-now-in-open-beta.html)

I am happy to announce that after many months of development and testing the new version 7 Folding@home client software is now available for open-beta testing. The V7 client is a complete rewrite of the previous client for Windows, OS-X and Linux with the following goals:

To make the installation and startup user-friendly for the novice.
To integrate the user interface into a single Monitor/Control program that manages the functionality previously contained in separate clients.
To create a forward-looking design that can be readily expanded to incorporate new Folding Cores without the need to issue new client releases.
To greatly improve previously problematic aspects including support for SMP, GPU, and the 3D viewer.

Getting Started
Please consider reading one of the guides listed in the documentation section, but if you want to dive right in you can start by downloading and installing the new client.

https://fah-web.stanford.edu/projects/FAHClient/chrome/site/FAHdownload.png (https://fah-web.stanford.edu/projects/FAHClient/wiki/BetaRelease)

Documentation
Install and user guides can be found here:

https://fah-web.stanford.edu/projects/FAHClient/
There are also some additional quick start FAQ items here
http://foldingforum.org/viewtopic.php?f=67&t=18043

Features
The new client has too many features to list but here are some of the highlights:

Improved Windows installer with support for Windows XP, Vista, 2008 and Windows 7.
64-bit OS-X install package. (32-bit in the works).
Debian/Ubuntu and RedHat/Fedora/CentOS 32-bit and 64-bit Linux packages.
Low priority background operation has very little impact on your computers usability. You should hardly notice Folding@home is running when using other applications.
A more compatible and stable 3D protein viewer with several view modes, rotation, zoom, online help and interpolated protein animations.
Separate but integrated console client (FAHClient), user interface (FAHControl) and 3D protein viewer (FAHViewer).
Novice, Advanced & Expert user interface modes. (See drop down list in FAHControl.)
Support for more than one Folding Slot (UNI, SMP or GPU).
Ability to monitor, configure and control many remote folding clients from a single computer.
Very low CPU overhead for FAHClient, FAHControl and FAHViewer. 3D viewer overhead can be minimized by disabling rotating and protein animation.
Single client for normal (Uniprocessor), SMP (Multiple CPUs) and GPU (Graphics Processors) folding.

Bugs/Tickets
The V7 client has undergone months of testing but due to the complex nature of distributed computing, the many features provided by the Folding@home client and the difficulties of simultaneously supporting software on Windows, OS-X and Linux there are still some open bugs, feature requests and likely other as of yet undiscovered issues. The beta testing process will help us test new features and fix any remaining bugs before we make a full public release. That said the open-beta V7 client is very usable and has many advantages over the previous client releases.

In an effort to increase the transparency of our development process we have decided to open read-only access to our bug tracking system. We are currently using Trac (http://trac.edgewall.org/), a Web based system which, among other things, manages a database of tickets. Each ticket represents either a bug or feature request of some component of the Folding@home client software. You can view the list of open tickets here:

v7 Client, Open Tickets Ordered by Milestone and Priority (https://fah-web.stanford.edu/projects/FAHClient/report/3)

Getting Help
Aside from the documentation the best place to get help is in a v7 client forum (http://foldingforum.org/viewforum.php?f=67). If you do have a problem post a message. There are many knowledgeable people ready and willing to help you but keep in mind we greatly appreciate thorough reports delivered by patient people who can keep a cool head even when things go wrong.
Final Notes
We are very excited to see this software make its way around the world improving and expanding Folding@home and thereby increasing our understanding of how proteins fold and ultimately helping to find cures for some of our societies scariest diseases. We greatly appreciate your participation and understand that without your generous contributions of time and computing resources there would be no Folding@home.

So dive right in and let us know about your experience.
PS You can find more information at this forum thread
http://foldingforum.org/viewtopic.php?f=67&t=18034&start=0

Blacksmith1

03-29-2011, 10:50 PM

Yay!!! the V7 is almost done. don't know if I want to try it yet but i'm thinking about it. gotta see about transfering my current WU's to it so i don't lose the work on my SMP.

slugbug

03-30-2011, 02:12 AM

Finally GPU support with Ubuntu working for anyone who uses Linux. ATI folding apparently works too. Anyone with an ATI card care to try this?

Blacksmith1

03-30-2011, 02:50 AM

I can't get this thing to take my GPU clients... it's running (I think) the SMP from 0%, but when I try to add the GPU "slots" it saves them and won't run them????
ok it's not saving them. So much for the new client being easy to use. I'm following the instructions, and it's not doing what it's supposed to.

James86

03-30-2011, 03:50 AM

It only supports 5k or newer on the ATI side and I have a 4850 so no go for me maybe Rob or Zac can post some #

Leganfuh

03-30-2011, 08:12 PM

Rob

03-30-2011, 08:23 PM

It only supports 5k or newer on the ATI side and I have a 4850 so no go for me maybe Rob or Zac can post some #

I should be able to test it out soon. I always forget to leave my PC on at night to do some Folding. I'll try to remember to do it tonight.

James86

03-30-2011, 08:54 PM

hopefully you can churn out some good #'s

Rob

03-30-2011, 09:06 PM

hopefully you can churn out some good #'s

We'll see. If they've retooled the way F@H interacts with AMD cards, we could see quite an improvement. From what I've read that's going to take considerable effort on the part of F@H due to the way AMD changed their API. (I think API is the right word.) From my limited experiences with F@H and my 6950, work unit-crunching was pretty darn slow.

zachig

03-30-2011, 10:03 PM

Rob...let us know when you try it. I might give v7 beta a try as well ;-)

Sent from my iPod touch using Tapatalk

ET3D

03-31-2011, 12:16 AM

Just installed the beta client, running with my (underclocked) 5850, and WU time estimate is around 10 hours, which isn't much different than before (a little slower, but it's just an estimate, and dropping faster than real time). Of course, the WU itself may be different. I'll let you know when there are some real results.

I do see a difference in that when I run AMD System Monitor I see that the GPU is at 98-99% utilisation, and before that it was lower (don't remember exactly, but I think in the 70-80%).

Leganfuh

03-31-2011, 02:16 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande March 30, 2011

Server updates completed, back on line (http://folding.typepad.com/news/2011/03/server-updates-completed-back-on-line.html)

fah-web.stanford.edu and the stats updates are back on line.

James86

03-31-2011, 04:37 AM

thebluebumblebee

03-31-2011, 07:03 AM

It only supports 5k or newer on the ATI side and I have a 4850 so no go for me maybe Rob or Zac can post some #

Pre 5xxx series support is not supposed to end until September. It will just run GPU2, so EV's will be needed.

GPU Slot Requirements
Windows XP or newer
1 or more supported GPU video cards
ATI/AMD
(GPU2 - fahcore_11)
2xxx series or newer
10.x AMD device driver or newer
(GPU3 - OpenCL - fahcore_16)
OpenCL compatible GPU, 5xxx series or newer
11.x AMD device driver or newer

ET3D

03-31-2011, 08:37 AM

First WU took about 6 hours. Second is expected to take about the same time. No stats yet regarding the points for this WU, but if it's similar to those I got with the old client then there's no significant gain in performance.

Edit: No wonder it didn't go up. It's a new client but still the same fahcore 11. Strange that GPU utilisation looked higher. Says here (http://folding.typepad.com/news/2011/03/fah-support-for-ati-gpus.html) "ATI core 16 will be publicly released after the v7 client is released, as the core needs the new client." So I guess I'll have to wait a little longer. I guess my observation about GPU utilisation was just wishful thinking.

Rob

03-31-2011, 04:25 PM

Rob...let us know when you try it. I might give v7 beta a try as well ;-)

Sent from my iPod touch using Tapatalk

I still haven't had a chance to do any Folding. I got home very late last night and spent only 10 minutes on my PC. Then I brushed my teeth and hit they hay. We'll see about tonight.

thebluebumblebee

03-31-2011, 05:03 PM

If you Fold on ATI, please read this post (http://en.fah-addict.net/articles/articles-1-3+gpu-environment-variables.php). This will apply until fahcore_16 comes out for ATI. That post is from August, 09, but I see posts (http://foldingforum.org/viewtopic.php?f=51&t=9162&start=240) going back to March of 09 about them.

Leganfuh

03-31-2011, 11:08 PM

ET3D

04-01-2011, 01:24 PM

Blacksmith1

04-02-2011, 02:56 AM

Any one get the v7 to run smp and gpu2 yet? I couldn't get it to work for me. SMP was fine but I couldn't get the gpu slots to go.

ET3D

04-02-2011, 05:32 AM

With the new GPU client I'm getting an estimated points per day of 4327.55. That's an estimate before even one WU has finished (updating the driver broke my previous WU). It's about twice what I got with the previous GPU client, so it's a good improvement. I hoped it would be even faster, but it's early days for this client so hopefully it will become even faster in the future.

Blacksmith1, what was the problem? I added a GPU slot, in the extra options I added 'client-type' = 'advanced', and it worked.

Blacksmith1

04-02-2011, 05:20 PM

this time I stated with the GPU client as prefered and added the smp. it worked. i think I have the advmethods switch in the right place??? I guess i'll find out. but i need to finish my current SMP WU before making the switch.

Leganfuh

04-05-2011, 08:52 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

April 05, 2011

Change to the stats system (http://folding.typepad.com/news/2011/04/change-to-the-stats-system.html)

There are some changes to the stats system which are needed for consistency between the web site stats (eg http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userstats) and the flat files (eg http://fah-web.stanford.edu/daily_user_summary.txt.bz2). The main issue is how we handle passkeys and their impact on donor rankings. I want to stress that this will not change point values or anything other than how we list the ordering of donors in our ranking.
Passkeys (http://folding.stanford.edu/English/FAQ-passkey) are a relatively recent addition to Folding@home. The passkey, a new feature beginning with the v6.0 FAH client, is a unique identifier that ties your contributions directly to you (not just those with your donorname). The use of a passkey prevents others from cheating using your name.
In order to have the stats flat files match the web site in terms of donor ranking, we need to change both the flat files and the web site. The issue is how we handle passkeys. The web site ignores accounts with passkeys right now (needed to do a fast SQL count(*)), whereas the flat files aggregates all passkey accounts into the same donor name and then orders by the aggregate points for that donorname.

Our proposal to fix this is to treat each donorname+passkey combo as a unique donor in terms of ranking in the flat files and web site. This would let the two be consistent. We've batted around alternatives and nothing else would fit the goals of being fast for the web site and consistent between the two. We will not of course give out the passkey in the file, although we are planning on distinguishing passkeys by revealing the last 2 digits. This should be enough to identify different accounts without giving away any critical information.

In the next few days, we will release flat files with the additional donorname + passkey info. After May 1, we will transition the FAH web stats to use the same method. This lag between the two is intended to give 3rd party stats a chance to update their scripts, if they choose.
I want to stress that 3rd party stats could choose to aggregate in the old way or the new way. We are making this change mainly so that the stats we present are consistent.

Leganfuh

04-06-2011, 12:29 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay PandeApril 05, 2011

More transparency in testing (http://folding.typepad.com/news/2011/04/more-transparency-in-testing.html)

For 10 years, we have rolled out Folding@home work units (WUs), Cores, and client software using a Quality Assurance (QA) protocol that involves several steps, including internal testing (int), closed beta testing (bet), open beta testing (adv), and full release (fah). The goal of this gradual rollout is to try to keep problematic WUs and software from getting released and to allow donors to have some choice in terms of how bleeding edge they’d like to be.

However, this does mean that a great deal of work is done in closed testing, which has several disadvantages. First and foremost, all the work that beta testers, Forum Moderators, and the Pande Group does to QA WUs is never seen. This also means the rationale for releasing WUs in their current form is not broadly visible. And while entry to the team of donors working on closed beta testing was always available, that is a large bar to cross just to see what's going on. On the other hand, there are many upsides to closed testing however, including having a tight knit group of knowledgable donors giving useful feedback for strong QA of WUs.

While there are pros and cons of closed testing, I've decided that it is a good time to push for much more transparency in Folding@home in general, including closed beta testing. So, from now on, closed beta testing (bet) forum will be open for all to see. However, in order to keep strong QA, only beta team members can write in this forum (but as always, membership is open to those who are interested and dedicated to testing WUs).

My hope is that this will show all of the hard work that is done in testing WUs and will help answer questions about specific WUs that often come up. Also in this spirit, we have opened our v7 client bug tracker for read-only access so donors can see our progress with client development.

There's a tremendous amount of activity that goes on behind the scenes and I'm excited to open that up so the hard work that's been going on for a decade can now be much more visible (and hopefully better understood and appreciated).

Cirozorro

04-17-2011, 03:20 AM

I reconfigured the GPU slot with 'client-type' = 'advanced' and got a core 16 WU. That was a couple of minutes ago. I'll let you know how it goes.

Edit: Forgot to install an up to date Catalyst. I have 10.9. I do have the latest OpenCL SDK installed though. So far F@H seems to work fine, but I'll update to a new driver anyway.

How exactly did you reconfigure it for advance methods. I am trying to figure it out. It was easy for me to do this before on the old console version, but on version 7, I'm not sure. Did you go to configure, then click the slots tab, then edit the gpu, and then under extra slot options(expert) add your 'client-type' = 'advanced' . If so, did you have those apostrophes in there or not?

I haven't got any 16 WU yet, only 0x11.

At least I can fold with my 6850, wasn't able to get it to fold prior to installing V7. I have all the opencl drivers and I am running the latest catalyst 11.4(preview).

Leganfuh

04-17-2011, 04:28 AM

How exactly did you reconfigure it for advance methods. I am trying to figure it out. It was easy for me to do this before on the old console version, but on version 7, I'm not sure. Did you go to configure, then click the slots tab, then edit the gpu, and then under extra slot options(expert) add your 'client-type' = 'advanced' . If so, did you have those apostrophes in there or not?

I haven't got any 16 WU yet, only 0x11.

At least I can fold with my 6850, wasn't able to get it to fold prior to installing V7. I have all the opencl drivers and I am running the latest catalyst 11.4(preview).

http://foldingforum.org/viewtopic.php?f=67&t=18187

D0M1N4T0R

04-18-2011, 09:59 PM

Leganfuh, I have a question regarding the current contest going on right now. How is anyone supposed to reach no.1 on the folding chart if you're half a million PPD? Kind of seems unfair to offer a gtx 590 if nobody can even come close to beating you...

Leganfuh

04-19-2011, 04:52 AM

Blacksmith1

04-19-2011, 03:41 PM

How is anyone supposed to reach no.1 on the folding chart if you're half a million PPD?
he was at zero when the contest started. and there is always runner-up this month, and/or next months contest...

Cirozorro

04-19-2011, 10:10 PM

All you have to do is add more systems to the one's you have.

Very true, D0M1N4T0R if you can't make it up to Number 1 you can join the rest of us vying for Number 10 spot at around 26-28000 ppd. I am sure next month the prize will be allocated randomly(so don't worry). That's usually how scott has done it, at least for the contest I have been in. I always have a hard time meeting the post requirement to be entered in though. This forum just isn't active enough for me to find enough opportunities to chime in, and I hate posting for posting sake.

I figure with only about 50 people to compete with, everyone will win something eventually.

D0M1N4T0R

04-20-2011, 02:45 AM

Cirozorro

04-20-2011, 04:51 AM

Well, I mean right now I have over 100 discrete computers folding for me and that's still not enough to even come close to Vijay. I don't have unlimited resources. Obviously this is about cancer research and not just winning stuff, but I don't realistically see myself going beyond second place this month, despite my massive growth over the past little bit. The whole thing just seems stacked towards people with insane money for folding/render farms.

A couple High level Nvidia cards and Intel CPU's(990x, drool) would be more than enough to do it. You get insane bonuses for bigadv WU. Leganfuh is one of the top folders(he individually is in the top 10). He isn't using hundreds of clients(only 19 (http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userpage&teamnum=41608&username=Leganfuh)) He deserves to win with those numbers, no render farm here.
He is getting an average of 2 million ppd with each one of his clients. Nothing but respect, and with a prize this nice, I don't blame him.( I only get 8k ppd with a quad amd, 7k with a radeon 6850, and I am seeing how the zacate e-350 folds right now.)

Blacksmith1

04-20-2011, 03:57 PM

not trying to be nasty, but this is getting wayyy :offtopic:, to the point of being :threadjacked:, so perhaps this conversation could be moved to it's own thread?

Leganfuh

05-01-2011, 06:24 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande

May 01, 2011

One physical server down (vsp09), bringing down CS's (http://folding.typepad.com/news/2011/05/one-physical-server-down-vsp09-bringing-down-css-.html)

One physical machine (vsp09) is down, bringing down all of its related VM's (vsp09*). We're working on it and hopefully will be able to get it back up today, unless there's a more serious issue.
UPDATE: The machine is now back up and the main CS (vsp09a) is running. We are keeping the other CS's down, since the other CS's are now obsolete and have been integrated into vsp09a.

Leganfuh

05-17-2011, 04:05 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
(c) 2007 Vijay Pande May 16, 2011

Best Practices FAQ (http://folding.typepad.com/news/2011/05/best-practices-faq.html)

Folding@home (FAH) is a major scientific endeavor, but is also a kind of contest for some donors to see who can donate the most points. In order to keep a sense of fair competition, we asked donors to help us establish a list of rules, summarized on this FAQ page: http://folding.stanford.edu/English/FAQ-BestPractices .
These rules are stated below to engender the spirit of competition in a way that is impartial for all donors. We thank everyone for their contributions and hope they will enjoy competing and donating to the project.

Leganfuh

06-16-2011, 01:43 AM

Folding@home (http://folding.typepad.com/news/)

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

June 15, 2011

update on v7 client progress (http://folding.typepad.com/news/2011/06/update-on-v7-client-progress.html)

It's been a little while since our last v7 beta release (v7.1.24) and so I wanted to give donors some sense of what's going on. We've been working on internal testing of two releases past the current beta release and fixing bugs along the way. While we could in principle release v7.1.25 to open beta, there are enough todo items that we've decided to hold off a bit until it's a bit cleaner and further along. However, we're not going to hold off forever of course, just long enough for our developers to make some significant progress, especially since doing a release generates a lot of feedback, which takes developers away from coding.
To give some sense of where we are, here's the internal release notes for two recent builds (v7.1.25 and v7.1.26). Note that v7.1.26 is still in progress. Also, the #'s after the comment refer to our bug tracker. We have opened up the bug tracker (https://fah-web.stanford.edu/projects/FAHClient/report/3), so one can see progress directly there on a daily basis if you're interested.

v7.1.26 (still under development):
* Failed upload attempt could cause WU to dump before it was expired. #679.
* Added AMD Radeon HD 6600 Series to GPU white-list.
* Fix failure to restart FAHControl in OSX when 'start minimized'. #649.
* Fixed a socket bug that could cause the loss of the end of a message.
* Build OSX client in 32-bit mode with Intel compiler.

v7.1.25:
* Hide 'Quit on window close' option in OSX.
* Fixed some problems with WU assign time and time offset calculations.
* Detect and ignore invalid assign time from older WS.
* Log computed WS time offset.
* Removed warning from Slot configuration about changing threads mid-run.
* Catch and log error accessing battery info in /sys on Linux
* Fix grayed out name and IP in client add after viewing local client. #640.
* Remove 'RS480 PCI-X Root Port' from GPU whitelist. #635
* Added a few new Radeon HD 6xxx cards.
* Added Nvidia GTX 590 device ID 0x1088 to whitelist.
* Increase Radeon HD 5xxxx and 6xxxx GPU type level by one. #653.
* Don't fail WS connections if all data was recieved even on net error.
* Print IP Address with 'Uploading' message.
* Fixes for OSX minimize and quit bugs. #649 & #659.
* Limit max CPUs per slot to system count. #652.
* Attempt to fix #654.
* Release system resources when querying OSX battery status. #650.
* Don't send 'auth' command from FAHControl if empty. #658.
* Fixed 'slot-add' NULL pointer exception. #666.
* Fixed 'log-updates start' error. #671.
* Fixed FAHClient script parsing bug. #676.
* Show 'Remote Access' tab in advanced mode. #648.
* Don't allow minimizing to sys-tray if it is not there. #670.
* Also print core return code numbers in hex. #677.
* Print times in ISO 8601 format. #664.
* Expire WUs in sending status.

Leganfuh

06-23-2011, 03:15 AM

http://www.bjorn3d.com/forum/images/icons/icon1.png

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)June 22, 2011

Changes to donor ranking on the Stanford stats web pages (http://folding.typepad.com/news/2011/06/changes-to-donor-ranking-on-the-stanford-stats-web-pages.html)

We have been making changes to the donor ranking on the Stanford stats pages to work to reconcile them with the 3rd party stats. The central issue at hand is how does a given stats system handle accounts with multiple passkeys. A more detailed discussion can be found in this discussion thread (http://foldingforum.org/viewtopic.php?f=16&t=17971&start=16).
We are working directly with 3rd party stats to come up with a solution that works for all. For now, we have made one change which brings them closer, but not completely in agreement. However, donors who pay close attention to the Stanford site will likely see a big change in their ranking. We're posting this blog post to give donors a heads up on this issue and some information of what's going on behind the scenes.

Leganfuh

06-26-2011, 06:31 PM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu (http://folding.stanford.edu/)
June 25, 2011

Stats db reset this morning – stats updates running again now (http://folding.typepad.com/news/2011/06/stats-db-reset-this-morning-stats-updates-running-again-now.html)

The stats db hung last night around midnight pacific time. We saw that it was down this morning (we get emails from the stats system when there hasn't been an update in over 2 hours) and we restarted the stats db. A stats update is now in progress and should continue to run.
We will keep an eye on this over the weekend in case there's some greater systemic problem here. Please note that we have a reduced admin staff on the weekends, so response will be a bit slower.

Leganfuh

07-03-2011, 06:51 PM

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

July 02, 2011

Change in the points system for bigadv work units (http://folding.typepad.com/news/2011/07/change-in-the-points-system-for-bigadv-work-units.html)

For new bigadv WUs, we have changed how the points are calculated to bring them back into balance with the rest of the points in Folding@home. There are more details in this post:
http://foldingforum.org/viewtopic.php?f=24&t=19059
The main jist of the change is that we are decreasing the points associated with bigadv WUs, from 50% over SMP to 20% over SMP. As with previous points changes, this deals with only new WUs to go out, not with WUs that have be collected, etc. I want to stress that the bigadv program is still continuing, but that, as we've mentioned before, this is an experimental program and subject to changes.
It's clear that any change to the points system is controversial, but this one has been raised as a very serious problem by many donors. After investigating the issues raised, we agreed that this was significantly out of balance, and made this change. Moreover, the feedback we have gotten is that we make a change soon and do so quickly, like "removing a bandaid" rather than drag out the pain. I'm sorry to have to make any changes at all, since any change is disruptive, but we (and many donors) felt very strongly that this change was very important.
The other change that we have in mind to do is to bring all classic and GPU WUs into the Quick Return Bonus (QRB) system. This would help further bring all FAH projects into balance. There may be some issues with GPUs and QRB, so we are looking to see what we can do to minimize problems with that before making a change in the points for GPU WUs.
Finally, I would like to remind all that we do listen to donors and take their input very seriously. There has been extensive discussions about the problems with the points system with the huge PPD's seen with bigadv (sometimes reaching 500,000PPD) and the lack of QRB for GPUs being major shortcommings.
Considering the great variety of donor opinions on this matter, it is no surprise that we agree with some donors and disagree with others. Moreover, with points, there will never be any system which makes everyone happy, but our goal is to try our best to balance the project as a whole, taking donor input seriously, and making hard calls when we feel it is necessary. This was definitely a hard call, but hopefully in time donors who disgaree now will come to understand the issues raised by the other donors and appreciate their point of view.

Blacksmith1

07-03-2011, 07:01 PM

Not to offend anyone,but it's about time. the points thing has stuck in my craw since they first started giving those huge bonuses to the bigadv projects. of course I was more than happy to take my SMP bonuses which those on gpu only or uni clients probably thought was unfair.

James86

07-03-2011, 07:40 PM

we might see a big drop in Leg's PPD

Blacksmith1

07-03-2011, 07:52 PM

Not so much, this is more to slow down the guys that are doing the magny-cours servers and getting 500,000 PPD from one box, Mike's farm should still produce a decent amount of PPD ( tho' it will take a hit)

Leganfuh

07-26-2011, 10:10 PM

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

July 25, 2011

New serverstats page

(http://folding.typepad.com/news/2011/07/new-serverstats-page.html) We've developed a new serverstat page (http://fah-web.stanford.edu/pybeta/serverstat.html), which we're now suggesting as a replacement for the old one (http://fah-web.stanford.edu/serverstat.html). The new one is more asthetically pleasing but also has a lot of changes under the hood to allow for more reliable and faster updates.
We're keeping the old serverstat page link pointing to the old page (i.e. no change) in case there were scripts that were parsing the old page. However, we've set the new page to update every 10 minutes and the old one to only update every hour. We will keep the old page up for at least two months to give 3rd party utilities a chance to update their code and to give us feedback (please post feedback to http://foldingforum.org ).

Leganfuh

08-07-2011, 08:24 PM

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

August 05, 2011
Results page updated – new key result published in our work in Alzheimer's Disease (http://folding.typepad.com/news/2011/08/results-page-updated-new-key-result-published-in-our-work-in-alzheimers-disease.html)
We have made a major update to the Results page (http://folding.stanford.edu/English/Papers) on the Folding@home web site (http://folding.stanford.edu/). We now list 95 papers that have directly resulted from Folding@home, although we note that there are 193 papers (http://folding.stanford.edu/Pande/Papers) from the Pande group in general. There are many new results to talk about, but I will just highlight a few below.
One major result is in the area of Alzheimer's Disease (paper #95). It is believed that Alzheimer's Disease results from the misfolding of the Abeta peptide. Understanding how Abeta misfolds could give us some key insights into how to cure Alzheimer's Disease. This paper experimentally tests a key prediction made in an earlier paper (paper #58: "Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach" by Nicholas W. Kelley, V. Vishal, Grant A. Krafft, and Vijay S. Pande. J. Chem. Phys. 129, 214707 (2008); DOI:10.1063/1.3010881). In this paper, we show experimentally that there appears to be a beta turn in the Abeta as predicted. This leads to a very stable form of misfolded Abeta which could be used as a starting point for a new Alzheimer's therapy. We are heavily pursuing this research direction at the moment.
Another key result is in the area of methods (paper #93). We are constantly honing our methods to improve Folding@home's ability to predict the behavior of proteins. This paper demonstrates the current state of the art in terms of both sampling and analysis. When compared to detailed TTET experiments, we show that our methods can piece out even fairly detailed aspects of folding. However, we also see the ways in which our models are not perfect, suggesting how we can improve our methods even further.
We'll highlight other papers as time goes on. I'm particuarly excited about these results. In particular, the results from paper #95 were first discovered several years ago, but we carried out several followup studies to verify them, etc. As always, I'm most excited about what we're doing now and hope to get some of our current key results in theses areas out from peer review soon.

Saryn

08-07-2011, 08:57 PM

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

Blacksmith1

08-07-2011, 09:11 PM

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

Saryn

08-08-2011, 01:26 AM

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

08-11-2011, 07:21 AM

Folding@home (http://folding.typepad.com/news/)

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu
(http://folding.stanford.edu/)
(c) 2007 Vijay Pande

August 10, 2011

2012 Michael and Kate Bárány Award

(http://folding.typepad.com/news/2011/08/2012-michael-and-kate-b%C3%A1r%C3%A1ny-award-.html) 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 (http://www.biophysics.org/AwardsOpportunities/SocietyAwards/MichaelandKateB%C3%A1r%C3%A1nyAward/tabid/504/Default.aspx) for Young Investigators from the Biophysical Society (http://www.biophysics.org/) 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 (http://folding.stanford.edu/English/Awards).

Blacksmith1

10-01-2011, 07:17 PM

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 (http://twit.tv/show/futures-in-biotech/85). 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

10-16-2011, 07:54 PM

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 (http://foldingforum.org/viewtopic.php?f=67&t=19795&sid=1f440f792d7719823b5fbd1b8340238b). 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/2011/10/update-on-the-v7-client-v7138-is-now-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 (http://en.wikipedia.org/wiki/Anton_(computer)) 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 (http://en.wikipedia.org/wiki/Folding@home) and a very impressive special purpose computer from DE Shaw Researched, called ANTON (http://en.wikipedia.org/wiki/Anton_(computer)). We're often been asked "how do they compare (http://foldingforum.org/viewtopic.php?f=15&t=16388&p=197134#p197134)?" 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 (http://pubs.acs.org/doi/abs/10.1021/ja106936n), instead of microsecond (http://www.sciencemag.org/content/330/6002/341.short) folding events over a single long trajectory) and 2) it can give statistically significant results on those long timescales.

http://folding.typepad.com/news/2011/10/comparison-between-fah-and-antons-approaches.html
Some interesting stuff for those who like info on the F@H program

thebluebumblebee

11-16-2011, 12:45 AM

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

11-16-2011, 02:23 AM

bumbleblee

11-16-2011, 05:45 AM

Well that sucks the big one :ahhhhh: 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

11-16-2011, 06:21 AM

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

11-16-2011, 06:44 AM

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

11-16-2011, 03:28 PM

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

11-16-2011, 07:15 PM

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

11-16-2011, 07:28 PM

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

Blacksmith1

11-17-2011, 03:32 AM

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.

Joshua_Mahr

11-17-2011, 03:40 PM

Well said Black!!

ET3D

11-18-2011, 04:47 PM

I understand why Scott is doing it, and have no problem with it, but it was just to illustrate that in the end points still matter in many cases, which are not directly related to F@H, but rather to the communities built around it.

Regarding bigadv, the limitation of number of cores is arbitrary, and I don't understand why it's necessary. If someone can hit the deadlines with a massively overclocked 6 core or 4 core, what's wrong with that?

Blacksmith1

11-18-2011, 09:40 PM

that's a question only the powers that be at F@H can answer.

Blacksmith1

12-14-2011, 07:40 PM

December 13, 2011
Update on outage – FAH has been up as of Sunday, stats back on line now (http://folding.typepad.com/news/2011/12/update-on-outage-fah-has-been-up-as-of-sunday-stats-back-on-line-now.html)
Here's our (I think) last update on this recent outage. This was a major disaster at Stanford affecting the whole campus and I'm grateful for our team coming in on Sunday to get things back up. The workservers have been up since then and work and stats have been saved. The stats updating was put on hold until we can make sure everything looked ok. We've turned it back on. Please note that there is no stats loss while we turn off updates. People should see a big bump in their stats shortly. Thanks for bearing with us through this.

Blacksmith1

02-22-2012, 01:54 AM

I have been sorely lacking in my responsiblities here, and do appologize. many updates to post starting with;

February 07, 2012 Update on "bigadv-16", the new bigadv rollout (http://folding.typepad.com/news/2012/02/update-on-bigadv-16-the-new-bigadv-rollout.html) As we've mentioned earlier (http://folding.typepad.com/news/2011/11/planned-changes-to-big-advanced-ba-projects-effective-january-16-2012.html), we have been preparing changes to the bigadv system –– both an increase in the number of cores required (and a shortening of deadlines to match) and the release of some new bigadv projects. The motivation for the core changes is as follows:
Bigadv is intentionally intended for the most powerful machines, which makes it naturally a moving target. Our goal with bigadv is to utilize the most powerful segment of (CPU-based) machines in the FAH project to work on projects that are particularly large (memory utilization, upload/download requirement) and require a large amount of computation. We are all fortunate in that processors get faster over time, so the highest-performing tier of donor machines also gets faster over time. We have a lot of exciting science being enabled by FAH donors, and it takes place at all levels of computational requirement and performance sensitivity. So it wouldn't help the project to have 50% of machines running bigadv. But it also wouldn't be a good match to have some of the older and/or bandwidth-limited machines running these most performance-sensitive projects.
As previously announced, our plan is to shorten the deadlines of the BA projects. As a result, assignments will have a 16 core minimum. We've been developing the new projects for the new "bigadv-16". This development has taken a bit longer than we expected, but we are now completing internal testing and reading beta projects for bigadv-16. We are bringing a new server online for bigadv-16. It will start by offering a new class of bigadv projects, but we will soon add in a number of projects on the same server that are more similar to bigadv projects donors have already seen. We want to make these work units available for testing, but at the same time we are still examining the points yield of these bigadv projects. So the points valuation remains a work in progress; we may alter points, bonuses, and/or deadlines in the process of testing.
Please expect a beta announcement soon for testing these new bigadv-16 work units. Then, after the new bigadv-16 projects stabilize, we will bring the bigadv-12 projects into line (points, deadlines) with the bigadv-16 projects and convert all projects to bigadv-16. We are not sure of the timescale for this yet, as we'd like to test the new projects in a thorough manner. We will endeavor to be as transparent as we can regarding upcoming changes in the bigadv program. Bigadv-8 projects will likely be phased out (and indeed are mostly not being assigned at this time).
As a side note, we recognize that the number of cores is a somewhat crude measure for system performance. Long-term, we have some ideas on how we'd like to improve this and use better metrics. But in the near term, we are using this admittedly imperfect metric.
Thank you for folding and for your support of the bigadv program and FAH more generally.

Blacksmith1

02-22-2012, 01:55 AM

February 11, 2012 stats back up – we're looking into missing interval (http://folding.typepad.com/news/2012/02/stats-back-up-were-looking-into-missing-interval.html) The stats system went down last night and is now back up. We are working on recrediting the WUs that came in last night. WUs coming in now should be getting credit as always.

Blacksmith1

02-22-2012, 01:56 AM

February 13, 2012 LTMD: Key new technology for accelerating folding and misfolding simulations in FAH (http://folding.typepad.com/news/2012/02/ltmd-key-new-technology-for-accelerating-folding-and-misfolding-simulations-in-fah.html)
Here's an update one one of our key projects looking into protein folding, performed in collaboration with Prof. Jesus Izaguirre's lab at Notre Dame. Below is an update from Prof. Izaguirre on the progress of this project.
The Izaguirre Lab at the University of Notre Dame (http://www.nd.edu/~lcls) has been collaborating with the Pande Lab at Notre Dame to produce a new GPU core that leverages the amazing speed of OpenMM (http://simtk.org/home/openmm) implicit-solvent force calculations (the heart of the GPU core in Folding@home) with new Long Timestep Molecular Dynamics (LTMD). This combination currently allows nearly a 10-fold speedup over OpenMM for systems as small as the WW domain (35 residues, 544 atoms) up to the Lambda repressor (80 residues, 2000 atoms). This translates into about 10 microseconds per day of simulation, which brings single trajectory millisecond simulations closer to FAH.
In collaboration with Cauldron Development (lead by Joseph Coffland, primary developer of the Folding@home client and also some cores), we hope to produce a GPU core that might be the first hybrid CPU-GPU core. There are technical questions on how to best do this, and we will engage our enthusiastic beta-tester GPU donors to discuss how to best approach this core when we are closer to production mode.
Going forward, we will continue to improve the LTMD GPU technology to obtain larger speedups for ever larger and biomedically relevant systems. A particularly excitement development will be the extension of LTMD GPU technology to explicit solvent simulations.
As far as scientific simulations, we are simulating the folding of about 80 mutants of the Pin1 WW domain, a protein implicated in some cancers and Alzheimer's disease. Understanding the role of mutations on misfolding can have important biomedical consequences, since many diseases have at least some component of misfolding of proteins. Another exciting project we are about to start is to simulate the dimerization during folding of proinsulin and proinsulin mutants, which results in some types of Type IA young and adult onset diabetes.
Thanks to the FAH donors, testers, and to the Pande Lab for their generosity and leadership which has allowed our technological developments and simulations to come this far.

http://nd.edu/~lcls/images/research/ww-domain.png

An image of the Pin WW domain.

Blacksmith1

02-22-2012, 01:56 AM

February 20, 2012 Update from Hong Kong University of Science and Technology (http://folding.typepad.com/news/2012/02/update-from-hong-kong-university-of-science-and-technology.html)
Here's a guest post from Prof. Xuhui Huang's lab at Hong Kong University of Science and Technology, another collaborating labortory in the Folding@home consortium. Prof. Huang and his lab have made several important methodological applications to FAH (for more details, see this review article (http://www.ncbi.nlm.nih.gov/pubmed/20421891)) as well as important research into the molecular nature of Huntington's Disease (http://www.ncbi.nlm.nih.gov/pubmed/19361448). Here's an update from Prof. Huang:
In the past a couple of years, the FAH has greatly helped us on our research on understanding the mechanisms of the molecular recognition processes. Molecular recognition, such as enzymes need to recognize their substrates and drugs have to be designed to specifically bind to certain receptors, is crucial to biology and medicine. Experimentally probing the chemical details of molecular recognition events is challenging, while computer simulations have the potential to provide a detailed picture of such events. With the help of the FAH donors, we are performing large-scale simulations on a group of Periplasmic Binding Proteins aiming to reveal the general relationships between protein structures, its intrinsic dynamics, and mechanism of recognition process.
The FAH projects related to the above research are between 7700 and 7712. We greatly appreciate the help from all the FAH donors, beta testers, and the rest of the FAH team to make our research on molecular recognition possible.

Blacksmith1

03-18-2012, 05:43 AM

February 24, 2012 Protein folding and viral infection (http://folding.typepad.com/news/2012/02/update-from-the-kasson-lab-at-the-university-of-virginia.html)
Understanding protein folding has many possible areas of biological and biomedical impact. For example, consider one of the major research areas of the Kasson lab at the University of Virginia, namely how the influenza virus infects cells. In the past, Dr. Kasson and Dr. Pande have studied two aspects of this (http://www.ncbi.nlm.nih.gov/pubmed?term=pande kasson influenza): how the influenza virus recognizes cell-surface receptors so it infects the "right" cell types and how small vesicles fuse.
http://upload.wikimedia.org/wikipedia/commons/thumb/4/48/PDB_1flc_EBI.jpg/220px-PDB_1flc_EBI.jpg
Dr. Kasson's group is now looking at the function of the viral protein that controls cell entry, a protein called hemagglutinin (http://en.wikipedia.org/wiki/Influenza_hemagglutinin). The hemagglutinin protein interacts with cell membranes: one piece inserts into the membrane, refolds, and alters the membrane in some unknown manner to promote viral entry. Another piece links the viral and cell membranes and refolds to bring the two together. We are running simulations on Folding@Home to examine each of these pieces. Dr. Kasson's laboratory also looks at these processes experimentally.
Both of these problems involve protein folding. This extends the problem of understanding folding beyond the "canonical" model of an unstructured protein in water taking on a final shape but instead in the first case a small protein inserting into a lipid membrane and changing shape in response to its environment and in the second case a large protein changing from one shape to another in response to physiological cues. One could consider these special cases of protein folding or how viruses use protein folding to infect cells.
Future posts will address methods we have developed to assist in these studies as well as other important problems we work on. We are also doing methodological work that will improve the efficiency of running Folding@Home simulations and analyzing the results. The Folding@home community has made an important contribution in providing the computing power for these studies (you can see some of our published work on the FAH papers page), and we are grateful to all involved

Blacksmith1

03-18-2012, 05:47 AM

February 27, 2012 New methods for computational drug design (http://folding.typepad.com/news/2012/02/new-methods-for-computational-drug-design.html)
A key aspect of Folding@home research has been using computational methods to design new drugs, especially for Alzheimer’s Disease. At the University of Virginia, the Shirts lab is developing methods to leverage the power of Folding@home to develop new drugs to fight disease. Generally, small molecules work as drugs by binding very specifically to certain locations on important proteins. For example, an antibiotic works by binding to a protein on a bacteria, thus interfering with the pathogen's internal workings seriously enough to disable or kill it. By targeting only protein sites that are unique to the pathogen, drugs can act extremely specifically, rather than harming the human body or desired microbes. The exact same principles can toggle very specific parts of our own body's protein machinery on or off, allowing development of drugs that fight diseases of caused by breakdown, mutation, or malfunction our own cellular machinery, like Alzheimer’s Disease, heart disease, diabetes, and many other conditions.
However, it is very hard to calculate exactly how tightly a given small molecule will bind to a target protein, or even exactly where and by what mechanism it will bind. A number of computational methods are used in industry today to estimate the binding affinity of small molecules in the process of drug design, but they mostly rely on approximations that are computationally cheap and very approximate, rather than more expensive methods that have the potential to be much more accurate. With Folding@home, we now have the capability to perform rigorous evaluations of these more complete methods, understand their limits, and make them more efficient and reliable.
We have been developing our methods working mostly with well-understood model systems, such as FKBP, a protein on the immune system signaling pathway. Once the methods are well-understood, we will be moving on try to design small molecules to treat AIDS (the HIV reverse transcriptase enzyme, required for DNA to replicate) and influenza (various proteins involved in virus cell entry). Such molecules will still require significant effort to make into drugs, since drugs also have to dissolve easily, penetrate cells, and not be broken down to quickly, but being able to predict more easily which molecules interact tightly with the intended targets will be a huge step in the right direction.
As part of our efforts to improve Folding@home infrastructure, we are also working to port new versions of the Gromacs molecular simulation platform to Folding@home and improving the interface and integration between Gromacs and Folding@home.

Blacksmith1

03-26-2012, 02:16 AM

March 20, 2012 Stanford scientists and collaborators boost potency, reduce side effects of IL-2 protein used to treat cancer (http://folding.typepad.com/news/2012/03/stanford-scientists-and-collaborators-boost-potency-reduce-side-effects-of-il-2-protein-used-to-trea.html) Today, I'm highlighting the work primarily out of Chris Garcia's lab (http://garcia-lab.stanford.edu/Welcome.html)at Stanford Medical School. The Garcia lab had a very exciting idea on how to re-engineer a very important protein and the Pande lab played a part by providing computer simulations to help understand the mechanism by which the new protein worked. The results are very exciting. Check out the link below for more details.
http://medicalxpress.com/news/2012-03-scientists-boost-potency-side-effects.html
SUMMARY. The utility of a naturally occurring protein given, sometimes to great effect, as a drug to treat advanced cancers is limited by the severe side effects it sometimes causes. But a Stanford University School of Medicine scientist has generated a mutant version of the protein whose modified shape renders it substantially more potent than the natural protein while reducing its toxicity.

Blacksmith1

03-26-2012, 02:19 AM

March 21, 2012 FAH simulations lead to a new therapeutic strategy for Alzheimer's Disease (http://folding.typepad.com/news/2012/03/fah-simulations-lead-to-a-new-therapeutic-candidate-for-alzheimers-disease.html) I'm very excited to finally talk about some key new results from our lab. These results have been a long time in coming and in many ways represents a major achievement for Folding@home (FAH) in general, demonstrating that the approach we started 10 years ago can make significant steps forward in our long term goals.
Specifically, our long term goals have been to 1) develop new methods to tackle the computational challenges of simulating protein folding; 2) apply these methods to gain new insights into protein folding; 3) use these methods and new insights to simulate Aß protein misfolding, a key process in the toxicity of Alzheimer's Disease (AD); and finally 4) to use those simulations to develop new small molecule drug candidates for AD. In the early years of FAH, we concentrated on the first two goals above. In the last 5-7 years, we have worked to accomplish the third goal. I'm now very excited to report our progress on the last goal –– using FAH for the development of new therapeutic strategies for AD.
In a paper just published in the Journal of Medicinal Chemistry (http://pubs.acs.org/doi/abs/10.1021/jm201332p?prevSearch=pande&searchHistoryKey=), we report on tests of predictions from earlier Folding@home simulations (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674793/), and how these predictions have led to a new strategy to fight Alzheimer's Disease. While this is not a cure, it is a major step towards our final goal, some light at the end of the tunnel.
The next steps, now underway in our lab, are to take this lead compound and help push it towards a viable drug. It's too early to report on our preliminary results there (I like to only talk publicly about work after it's passed through peer review), I'm very excited that the directions set out in this paper do appear to be bearing fruit in terms of a viable drug (not just a drug candidate). I hope I'll have more to say in the coming months!

Design of β-Amyloid Aggregation Inhibitors from a Predicted Structural Motif
Paul A. Novick†, Dahabada H. Lopes‡, Kim M. Branson†, Alexandra Esteras-Chopo§, Isabella A. Graef§, Gal Bitan‡, and Vijay S. Pande†*
† Department of Chemistry, Stanford University, Stanford, California 94305, United States
‡ Department of Neurology, UCLA, Los Angeles, California 90095, United States; Brain Research Institute, UCLA, Los Angeles, California 90095, United States; Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
§ Department of Pathology, Stanford University, Stanford, California 94305, United States
*Corresponding author.

Abstract
Drug design studies targeting one of the primary toxic agents in Alzheimer’s disease, soluble oligomers of amyloid β-protein (Aβ), have been complicated by the rapid, heterogeneous aggregation of Aβ and the resulting difficulty to structurally characterize the peptide. To address this, we have developed [Nle35, d-
(http://folding.typepad.com/.a/6a00e54ef157d78834016302ec4716970d-pi)Pro37]Aβ42, a substituted peptide inspired from molecular dynamics simulations which forms structures stable enough to be analyzed by NMR. We report herein that [Nle35, d-Pro37]Aβ42 stabilizes the trimer and prevents mature fibril and β-sheet formation. Further, [Nle35, d-Pro37]Aβ42 interacts with WT Aβ42 and reduces aggregation levels and fibril formation in mixtures. Using ligand-based drug design based on [Nle35, d-Pro37]Aβ42, a lead compound was identified with effects on inhibition similar to the peptide. The ability of [Nle35, d-Pro37]Aβ42 and the compound to inhibit the aggregation of Aβ42 provides a novel tool to study the structure of Aβ oligomers. More broadly, our data demonstrate how molecular dynamics simulation can guide experiment for further research into AD.

http://folding.typepad.com/.a/6a00e54ef157d78834016302ec4716970d-800wi (http://folding.typepad.com/.a/6a00e54ef157d78834016302ec4716970d-pi)

Blacksmith1

03-26-2012, 02:21 AM

March 22, 2012 Web page revamp and v7 rollout (http://folding.typepad.com/news/2012/03/web-page-revamp-and-v7-rollout.html) We're installing a new web page for our main site http://folding.stanford.edu (http://folding.stanford.edu/). While we're not done quite yet, the main changes are in. Hopefully the new site is cleaner and simpler, both in aesthetics and in ability to navigate.
http://folding.typepad.com/.a/6a00e54ef157d788340168e91ad23d970c-800wi (http://folding.stanford.edu/)This also coincides with our official rollout of the version 7 (v7) client software for Folding@home. This new client is a complete rewrite with the intention to make it much easier for donors to contribute to Folding@home. In particular, the new client unifies the classic, SMP, and GPU clients into a single download. Also, installation (especially of the more high performance clients such as SMP and GPU) is much easier than before. Finally, the revamped viewer should also be a much better user experience for FAH donors.
All in all, our hope is that these combined changes make it much easier for people to understand what we're about and to help contribute to Folding@home

Blacksmith1

07-16-2012, 05:26 PM

July 16, 2012-New GPU-powered algorithms (http://folding.typepad.com/news/2012/07/new-gpu-powered-algorithms.html)
Guest post from Dr. Xuhui Huang, Hong Kong University of Science and Technology
In this post, I want to introduce a new GPU-powered clustering algorithm we recently developed to analyze the large molecular dynamics simulation datasets generated by Folding@home. Folding@home can generate enormous sets of protein structures. A critical step in analyzing these large datasets involves some form of reduction in the dataset, usually in the form of clustering. We recently developed a GPU powered clustering algorithm using the intrinsic properties of a metric space to rapidly accelerate the clustering. Overall, our algorithm is up to two orders of magnitude faster than the CPU implementation, and holds even more promise with the ever increasing performance in GPU hardware.
This algorithm should facilitate numerous applications. For example, one of the systems we tested our code on is the human islet amyloid polypeptide (hIAPP) peptide, whose aggregation is implicated in Type 2 diabetes. We hope further analysis of this data will provide insights that will inform the development of treatments for diabetes.

Blacksmith1

07-23-2012, 10:55 PM

July 23, 2012-Bonus for A4-core based projects –– now in effect
A brief update to our previous blog post on the A4 bonus (http://folding.typepad.com/news/2012/07/bonus-for-a4-core-based-project.html): the bonus is now in effect.

the previous blog post;
Bonus for A4-core based projectsWe've noticed a significant number of high priority projects are trailing behind existing projects. Newer projects are aimed at interpreting and guiding experiments where the full power of Folding@home (F@h) is essential to continue pushing the boundaries of scientific and medical discoveries.
The main cause of this issue is the core version needed to run these simulations. Many of our newer SMP projects use the A4 core, which has several scientific advancements, while existing projects use the still important A3 core. The A4 core is not compatible with Clients below version 6.34 and many donors are still running these older Client versions.
This presents an opportunity to encourage people to donate their cycles towards these vital A4 projects. To emphasize the scientific importance of these work units, we are boosting the base points of all A4 work units by 10% when uploaded (Note that this bonus will not be reported by V7 or by the 3rd party applications which project PPD but the points will appear when your statistics are credited). The quick return bonuses will be calculated on top of the increased base points. This will start on Monday July 23, 2012, and we will keep this 10% bonus in effect for at least 3 months as a trial period, but plan to keep it longer, as needed.
To participate, donors should be running a recent version of the F@h Client. We strongly encourage Windows users to update to the much improved V7 Client. Although F@h Client v6.34 or newer is sufficient to participate for any supported operating system. Please note the Linux and OSX V7 Clients are a work in progress and feedback is welcomed.
v7 Clients:
Windows/Linux: Visit our home page, http://folding.stanford.edu/English/HomePage
Mac OSX: v7 for OSX is still in testing. For a beta copy: https://fah-web.stanford.edu/projects/FAHClient/wiki/BetaRelease

Old v6.34+ Clients
Windows/Linux: http://folding.stanford.edu/English/DownloadWinOther