Help Look For A Cancer Cure...

[Larry]

Reseachers at Stanford University are currently at work in a distributed computing project in their efforts to understand protein folding or human DNA replication, in effect trying to find a cure for cancer.

 

Distributed computing means that instead of using just one supercomputer to do the work, the Stanford researchers are creating a virtual supercomputer that is composed of over a million PCs all over the world. By distributing the work to hundreds of thousands of computers at a time, they are completing work that would take hundreds of years for a normal supercomputer to complete.

 

As of today there have been already 50 scientific papers that have been published in relation to DNA replication, all because of the folding @ home project.

 

You can be a part of this by downloading the folding@home client from Folding @ Home Client for Windows

 

the program runs in your computer's background and utilizes the unused portion of your PC's CPU since it is rarely ever used at capacity, for example if your computer uses 70% capacity while running your programs or surfing MTC, Folding@Home uses the remaining 30%.

 

The folding @ home client is totally safe from spyware and viruses and has been deemed so by hundreds of computer experts. Google and Sony have endorsed the folding @ home client.

 

for more information on the folding@home client and the Stanford University research you can visit these links:

 

Folding.Stanford.Edu

 

Folding@Home Wikipedia Entry

 

Also if you own a PS3 and it's connected to the internet, Sony has released a PS3 client for the Folding@home effort.

 

This is a chance to be a part of something that will eventually help us all, as the researchers come closer to finding the cure for cancer, diabetes, Alzheimer's, Parkinson's etc.

 

By joining this effort, your doing humanity's work. The ultimate reward would be better healthcare, and a brighter future for cancer victims.

 

If you can't download the client or for some reason can't install it in your home PC, help in your own little way. you can have a link to this thread in your signature or you can tell your other friends IRL, or on other boards about this.

Edited July 14, 2007 by Larry

[rdaq97]

i lost my mom to cancer. please support this initiative. I will do my part to help spread this movement. nice one bro.

[tom_babauta]

do i have to be online everytime, if i run the client

[Larry]

do i have to be online everytime, if i run the client

 

yes

 

if you run on dial up the F@H client can be configured to dial automatically, or wait until you connect.

 

OT:

 

Why is this thread here? I'm not asking a medical question nor am I consulting from medical professionals.

[Larry]

The Science of Folding@Home

 

from the F@H website:

 

WHAT ARE PROTEINS?

 

Proteins are necklaces of amino acids --- long chain molecules. Proteins are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions which make biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work?

 

 

 

RELATIONSHIP TO THE HUMAN GENOME PROJECT

 

Since proteins play such fundamental roles in biology, scientists have sequenced the human genome. The genome is in a sense a "blueprint" for these proteins -- the genome contains the DNA code which specifies the sequence of the amino acids beads along the protein "necklace."

 

 

 

WHY DO PROTEINS "FOLD"?

 

However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."

 

One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn how to make synthetic polymers with these properties. Movies of the results of some of these simulation results can be found here.

 

 

 

PROTEIN FOLDING AND DISEASE: BSE (Mad Cow), Altzheimer's, ...

 

What happens if proteins don't fold correctly? Diseases such as Alzheimer's disease, cystic fibrosis, BSE (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding.

 

When proteins misfold, they can clump together ("aggregate"). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimer's disease.

 

 

 

PROTEIN FOLDING AND NANOTECHNOLOGY: Building man made machines on the nanoscale

 

In addition to biomedical applications, learning about how proteins fold will also teach us how to design our own protein-sized "nanomachines" to do similar tasks. Of course, before nanomachines can carry out any activity, they must also be assembled.

 

 

 

WHY IS PROTEIN FOLDING SO DIFFICULT TO UNDERSTAND?

 

It's amazing that not only do proteins self-assemble -- fold -- but they do so amazingly quickly: some as fast as a millionth of a second. While this time is very fast on a person's timescale, it's remarkably long for computers to simulate.

 

In fact, it takes about a day to simulate a nanosecond (1/1,000,000,000 of a second). Unfortunately, proteins fold on the tens of microsecond timescale (10,000 nanoseconds). Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! That's a long time to wait for one result!

 

 

 

A SOLUTION: DISTRIBUTED DYNAMICS

 

 

To solve the protein folding problem, we need to break the microsecond barrier. Our group has developed multiple new ways to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way -- with a near linear speed up in the number of processors. Thus, with power of Folding@Home (over 100,000 processors), we have successfully smashed the microsecond barrier, simulating milliseconds of folding time and helped to unlock the mystery of how proteins fold.

 

 

 

WHAT HAVE WE DONE SO FAR AND WHERE ARE WE GOING?

 

 

Folding@Home has been a success. We have folded several small, fast folding proteins, with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions.

 

Since then, Folding@Home has studied more complex proteins, reporting on the folding of many proteins on the microsecond timescale, including BBA5, the villin headpiece, Trp Cage, among others.

 

More recently, we have been putting a great deal of effort into studying proteins relevant for diseases, such as Alzheimer's, Hunntington's, and Osteogenesis Imperfecta.

[Larry]

Results from the Folding@Home Project:

 

2005 First results from Folding@Home cancer project published.

 

We have been studying the p53 tumor surpressor and our first results on p53 have recently been published. You can find a summary and link to the paper on our papers page.

 

To our knowledge, this is the first peer-reviewed results from a distributed computing project related to cancer. Thanks to the continued support of FAH donors, this is will be just the first of many cancer related works that will come from FAH.

 

Roughly half of all known cancers result from mutations in p53. Our first work in the cancer area examines the tetramerization domain of p53. We predict how p53 folds and in doing so, we can predict which amino acid mutations would be relevant. When compared with experiments, our predictions have appeared to agree with experiment and give a new interpretation to existing data.

 

http://folding.stanford.edu/p53dimer.jpg

Structure of the p53 dimer with the Leu330 mutant highlighted. Our simulations predict several mutations which would have a signifincat impact on the rate of folding of p53. This one, Leu330, has already been implicated in cancer.

[Larry]

Folding @ Home FAQ

 

Who "owns" the results? What will happen to them?

Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's Chemistry Department), which is a nonprofit institution dedicated to science research and education. We will not sell the data or make any money off of it.

 

Moreover, we will make the data available for others to use. In particular, the results from Folding@home will be made available on several levels. Most importantly, analysis of the simulations will be submitted to scientific journals for publication, and these journal articles will be posted on the web page after publication. Next, after publication of these scientific articles which analyze the data, the raw data of the folding runs will be available for everyone, including other researchers, here on this web site.

 

How can I see how many other people are participating? What has been "folded" so far? And how much have I folded so far?

We keep many types of statistics of users and work accomplished on our web page. You can check out your Individual stats, Team stats, and overall project stats. Also, please check out the Results, Press, and Papers sections.

 

Why don't you post the source code?

Most of the critical parts of FAH are publicly available. The Tinker and Gromacs source codes can be downloaded and run. Unlike many computer projects, the paramount concern is not functionality, but the scientific integrity, and posting the source code in a way that would allow people to reverse engineer the code to produce bogus scientific results would make the whole project pointless.

 

What has the project completed so far?

We have been able to fold several proteins in the 5-10 microsecond time range with experimental validation of our folding kinetics. This is a fundamental advance over previous work. Scientific papers detailing our results can be found at papers.html. We are now moving to other important proteins used in structural biology studies of folding as well as proteins involved in disease. There are many peer-reviewed and published in top journals (Science, Nature, Nature Structural Biology, PNAS, JMB, etc) which have resulted from FAH. Current, more than all of the other major distributed computing projects combined!

 

Why not just use a supercomputer?

Modern supercomputers are essentially clusters of hundreds of processors linked by fast networking. The speed of these processors is comparable to (and often slower than) those found in PCs! Thus, if an algorithm (like ours) does not need the fast networking, it will run just as fast on a supercluster as a supercomputer. However, our application needs not the hundreds of processors found in modern supercomputers, but hundreds of thousands of processors. Hence, the calculations performed on Folding@Home would not be possible by any other means! Moreover, even if we were given exclusive access to all of the supercomputers in the world, we would still have fewer cycles than we do with the Folding@Home cluster! This is possible since PC processors are now very fast and there are hundreds of millions of PCs sitting idle in the world.

 

Can I run Folding@Home on a machine I don't own?

Please only run Folding@Home on machines you either own or on which you have the permission of the owner to run our software. Any other use of Folding@Home violates our license agreement (and just isn't a good idea in general).

 

What are the minimum system requirements?

All computers can contribute to Folding@Home. However, if the computer is too slow (eg wasn't bought in the last 3-4 years or so), the computer might not be fast enough to make the deadlines of typical work units. In this case, one should run with deadlineless work units.

[gerryandrada]

Miss my Nanay...

[kingfsx]

its hard to deal with this if its in someone you dearly love... hope one, cancer cure (for real) will be known to mankind... chemotherapy is way too hard for anyone who has this disease.

[cadr117]

anybody familiar with stem cell theraphy?

[Guest SCHIZOPRENIC]

anybody familiar with stem cell theraphy?

 

 

pampabata daw yan, don't have an idea where i heard that.. but i remember i get that number..

[Guest SCHIZOPRENIC]

my elder brother and my dad are both cancer patients. both my parents' side have cancer.

 

brother has an unknown cancer, founded in july 2005, rarely eats fish, never drinks liquor, excessive chain smoker before, undergone cobalt, chemotheraphy for only 3 sessions(sumuko na sya, hindi na nya nakayanan masakit na daw katawan nya sa gamot) :cry:

 

dad has a colon cancer founded in 1997 has undergone chemotheraphy for six sessions, no hair loss(unlike his sisters), only eats fish, rarely eats pork, never eats beef for all his life, for 40years he always drinks beer or hard liquor even though his diabetic(can't walk alone).

 

they died in 2006, my brother died 6months after the cancer was found and 6 months after my dad died from pneumonia. 3months after my uncle followed and my aunt in december 2006 in the states due to brain cancer.

[angel_by_day]

my elder brother and my dad are both cancer patients. both my parents' side have cancer.

 

brother has an unknown cancer, founded in july 2005, rarely eats fish, never drinks liquor, excessive chain smoker before, undergone cobalt, chemotheraphy for only 3 sessions(sumuko na sya, hindi na nya nakayanan masakit na daw katawan nya sa gamot) :cry:

 

dad has a colon cancer founded in 1997 has undergone chemotheraphy for six sessions, no hair loss(unlike his sisters), only eats fish, rarely eats pork, never eats beef for all his life, for 40years he always drinks beer or hard liquor even though his diabetic(can't walk alone).

 

they died in 2006, my brother died 6months after the cancer was found and 6 months after my dad died from pneumonia. 3months after my uncle followed and my aunt in december 2006 in the states due to brain cancer.

 

sir i strongly suggest that you have a total colonoscopy done.

and regular check-ups, of course.

[peterparker]

my elder brother and my dad are both cancer patients. both my parents' side have cancer.

 

brother has an unknown cancer, founded in july 2005, rarely eats fish, never drinks liquor, excessive chain smoker before, undergone cobalt, chemotheraphy for only 3 sessions(sumuko na sya, hindi na nya nakayanan masakit na daw katawan nya sa gamot) :cry:

 

dad has a colon cancer founded in 1997 has undergone chemotheraphy for six sessions, no hair loss(unlike his sisters), only eats fish, rarely eats pork, never eats beef for all his life, for 40years he always drinks beer or hard liquor even though his diabetic(can't walk alone).

 

they died in 2006, my brother died 6months after the cancer was found and 6 months after my dad died from pneumonia. 3months after my uncle followed and my aunt in december 2006 in the states due to brain cancer.

 

 

bro, how old are you na ba..?

 

i humbly suggest that you should think about cancer screening procedures kasi nga you have a strong family history...

 

and it would not help if you smoke, drink a lot, no exercise, or you have an unhealthy diet...

 

 

:mtc:

[peterparker]

anybody familiar with stem cell theraphy?

 

 

Stem cell treatments are a type of cell therapy that introduce new cells into damaged tissue in order to treat a disease or injury. Many medical researchers believe that stem cell treatments have the potential to change the face of human disease and alleviate suffering. The ability of stem cells to self-renew and give rise to subsequent generations that can differentiate offers a large potential to culture tissues that can replace diseased and damaged tissues in the body, without the risk of rejection.

 

A number of stem cell treatments exist, although most are still experimental and/or costly, with the notable exception of bone marrow transplantation. Medical researchers anticipate one day being able to use technologies derived from adult and embryonic stem cell research to treat cancer, Type 1 diabetes mellitus, Parkinson's disease, Huntington's disease, cardiac failure, muscle damage and neurological disorders, among others.

 

For over 30 years, bone marrow, and more recently, umbilical cord blood stem cells have been used to treat cancer patients with conditions such as leukemia and lymphoma. During chemotherapy, most growing cells are killed by the cytotoxic agents. These agents not only k*ll the leukemia or neoplastic cells, but also the haematopoietic stem cells within the bone marrow. It is this unfortunate side effect of the chemotherapy that the stem cell transplant attempts to reverse; the donor's healthy bone marrow reintroduces functional stem cells to replace those lost in the treatment. In all current stem cell treatments obtaining stem cells from a matched donor is preferable to using the patients own. If (always as a last resort and usually because no matched donor can be found) it is deemed necessary for the patients own stem cells to be used and the patient has not stored their own collection of stem cells (umbilical cord blood), bone marrow samples must therefore be removed before chemotherapy, and are re-injected afterwards.

 

 

 

:mtc: