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Stanford's goal: to understand protein folding, protein aggregation, and related diseases.

What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, and Parkinson's disease.

What does Folding@Home do? Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. Stanford uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct Stanford's approach to examine folding related disease.

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Recent FAH work on cancer: A brief overview
[H]ard|Folding Administrator

Posts: 98
Points: 2,740,038
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Posted: Thu Mar 27, 2014 03:20 am
New F@H team member Ms. Jingcheng Wu discusses recent F@H work.

Part I

Cancer affects the general population in an extensive and intensive way. It accounts for 1 out of 4 deaths in the US.1 The global annual cancer cases are expected to rise to 22 million within the next two decades.2 Existing drugs used in chemotherapy on the market are not only ineffective 97% of the time,3,4 but also cause severe damage to the body as a whole due to the drugs high toxicity. We are all too familiar with the frightening adverse effects of chemotherapy such as hair-loss, holes in intestine, swelling of the body, feeling sick and tired, abnormal bleeding, to name a few. Many cancer patients choose death over going through the agony of chemotherapy by refusing the treatments.

The reason behind the severe toxicity of anti-cancer drugs lies in their low selectivity. Aiming at killing cancer cells, the drugs also massively destroy normal cells and impede the growth of new healthy cells. Thus come the tragic sufferings very often seen in the oncology wards. The current cancer drugs attempt to cure the patients while kill them at the same time. The solution, then, lies in finding a new way of targeting cancer cells with minimal harm to normal cells.

Full Article here.

Part II

C-src is short for c-src tyrosine kinase. Kinase is a type of enzyme that removes a part (phosphate group) of the molecule (ATP) that is required for every energy-expending process in the body, and attaches it to a specific amino acid (tyrosine, threonine or serine) of a protein (substrate). C-src belongs to a family of kinases called the Src tyrosine kinase.

C-src stimulates the pathways that induce cell growth, generate new blood vessels, prevent cell suicide, and give cells ability to migrate1,2 all necessary to give rise to proliferation of invasive cancer cells. When there is a mutation to the gene that encodes c-src, mutant c-srcs produced could mimic the functions of the normal signal transduction c-srcs.3 When there is over or mis-expression of the said gene, too many normal c-srcs would be produced. In both cases, it is like stepping on a gas pedal of a car. Once the aforementioned abnormality is coupled with the loss of tumor suppressor gene functions,4 it is like additional loss of the brake of a car, and the car takes off and wreaks havoc.

Full Article: here.
Adding a completely new way to fold, directly in the browser.
[H]ard|Folding Administrator

Posts: 98
Points: 2,740,038
Work Units: 6,436

Posted: Thu Feb 27, 2014 08:49 am
Stanford is working on a new way to run F@H through a browser.

Through a collaboration with Google, the Huang lab at UST Hong Kong, and the Pande Lab at Stanford University, we’ve been working on a new way to run Folding@home –– through the browser. The primary goal here is to make folding much easier to run, especially for non-expert computer users.

Open beta. We are happy to announce that we now ready to release a first open beta test of the web client. It uses Google’s Native Client (aka NaCl) technology, allowing one to run Folding@home in a browser.

Full Article here.

Revised plans for BigAdv (BA) experiment.
[H]ard|Folding Administrator

Posts: 98
Points: 2,740,038
Work Units: 6,436

Posted: Tue Jan 28, 2014 09:47 pm
Stanford is revising it's plans for BigAdv.

Weve put a lot of time into reading the comments about the BA experiment and have come to some conclusions regarding how we should proceed. BA was originally conceived as an experiment to push FAH as close to what you could run on a traditional supercomputer as possible, doing calculations that most researchers thought could never run on a distributed computing platform. In order to make this possible, the requirements for BA would have to be pretty extreme and constantly updating (much like how supercomputers are constantly being updated to the latest hardware).

Full article: here.
Looking back at 2013 and forward to 2014.
[H]ard|Folding Administrator

Posts: 98
Points: 2,740,038
Work Units: 6,436

Posted: Mon Dec 30, 2013 07:08 am
Quite a bit of information from Stanford was released this month.

Looking back at 2013 and forward to 2014.

As the year ends, its a natural time to look at some key highlights of weve done in 2013 and look ahead to whats on deck for 2014. One of the challenges of science results can easily take a year for us to run on FAH, analyze, and publish. So, the work of 2012 comes out in 2013 and the projects running in 2013 get to reach the public in 2014. So, it makes sense to talk about both work thats been going on this year and how all of this will shape up in 2014. Weve been doing a lot behind the scenes in 2013 and Im excited about all of this getting out to the public in 2014. Here are some key developments.

FAH development in 2013. Weve had several new developments in how FAH works, from both the donor perspective as well as how FAH works behind the scenes. With the addition of new programmer Yutong Proteneer Zhao, Core 17 was a big advance for FAH. It brought the most advanced features from the OpenMM GPU code, especially major speed increases for AMD/ATI cards. Moreover, it also brought a natural path to true Linux GPU support and lots of useful scientific updates. The v7 client continues to advance, with a new web interface; these simplifications have been important especially for certain partners who have wanted to see an easier to use FAH client before they can help us push for greater deployment. Adaptive sampling approaches have been a part of how FAH works, but weve also been moving to automate this process, leading to more powerful ways we can use the power of the FAH clients.

Full Article: here.

Key new results published in Nature Chemistry

A key new work from the Pande Group just came out in Nature Chemistry and got a nice holiday present: our work on the cover!

Briefly, we applied methods developed and honed on Folding@home to Google Exacycle (Googles massively parallel cloud resource a lot like running Folding@home behind their firewall). The resources that Google donated to PG/Folding@home was pretty massive, allowing us to tackle a really significant and challenging problem in biology and drug design.

Full Article: here.

Changes to the bigadv threshold

We have a policy of periodically re-evaluating the bigadv program, including the threshold required to run bigadv projects.

It is the intent of bigadv to match large and resource-intensive work units with some of the most powerful machines used by FAH donors. This most powerful line naturally advances with computing power. To date, bigadv has been a CPU-based program, and with increasing numbers of CPU cores and power of those cores, we have decided to lay out a roadmap of bigadv threshold changes for the next several months.

Feb 17 (two months from today): bigadv threshold will become 24 cores

Apr 17 (four months from today): bigadv threshold will become 32 cores

Full Article: here.
Changes in Core17: update and move to full fah
[H]ard|Folding Administrator

Posts: 98
Points: 2,740,038
Work Units: 6,436

Posted: Mon Nov 25, 2013 07:36 pm
There are some new changes to Core 17.

Core17 Release Notes:

-Much more responsive exiting

-Fixed bugs related to visualization for next version of the FAHViewer

-Disabled some internal debug code

-For Windows NVIDIA Users running on a single GPU, weve enabled a new feature called temperature control that pauses the core internally. This is disabled by default.

-To enable temperature control, a pair of additional arguments are required:

-tmax (maximum temperature threshold in Celsius), must be less than 110

-twait (minimum wait duration in seconds), must be at least 900

-if temperature > tmax, then the GPU waits for at least twait seconds

-these can be passed in via extra-core-args in the config.xml file :

<slot id=0&#8242; type=GPU>

<extra-core-args v=-tmax=80 -twait=900&#8242;/>


-Removed dependency of glib.
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