Talk:Folding@home/Archive 3

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Archive 1 Archive 2 Archive 3

Journals for possible future citations

The article used to contain a long list of journal references. They were first added by User:Johnnaylor back in February 2008, and now contain almost everything needed in a journal citation. As I have now summarized the key points of some of the important papers, I had to comment the rest out. I haven't been able to include content from all them, because that would involve delving into unnecessary detail. So although they remained commented out at the very end of the article, the artice's byte count seems to include them, and this has been the cause of some confusion/misunderstandings for a couple of Wikipedians already. To alleviate probable future issues, I am moving all of them over here. If there is an publication that contains an important fact or point, feel free to cut and paste it from this section and use it as a citation in the article. Since the information in these journal citations can be a bit tricky to find, I didn't want to waste Johnnaylor's work. Thus here they are:

-Begin commented-out journal list

-End commented-out journal list

Jessemv (talk) 00:54, 18 November 2011 (UTC)

Does the lead need to be simplified?

I received an email today from a fellow Wikipedian who said that that the lead was too technical and should be simplified. He suggested something like the following should be added to the beginning or replace the first lead paragraph: "Folding@home is a distributed computing project at Stanford University which uses unused computing time on hundreds of thousands of home computers and gaming systems to help answer questions about diseases such as Alzheimer's, Parkinson's and various cancers. Anyone can donate computer time by downloading and installing the free software from the Folding@home website." However, I like the lead the way it is right now, and I feel that it follows WP:MOSINTRO and in general MOS:LEAD fairly well. Rosetta@home is the only article about a distributed computing project to achieve Good or Featured Article status, so it serves as a kind of guideline. R@h's lead describes the distributed computing concept in the first paragraph just like the above suggestion, while F@h describes it in the second paragraph. Should the lead be rewritten similar to the above suggestion? Thoughts? Jesse V. (talk) 01:00, 4 March 2012 (UTC)

I think the reading level of the lead is about right. It's important to avoid unnecessary jargon and not dive into unnecessary technical depth (especially in the lead), but I think the complexity of this article's introduction is on par with that of other featured articles on technical subjects, e.g. Parallel computing, RNA interference, Rosetta@home, etc. In my opinion the proposed revision to the first paragraph veers too much toward overtly recruiting new Folding@home volunteers. Emw (talk) 13:49, 18 March 2012 (UTC)
I agree. Thanks very much. Jesse V. (talk) 14:19, 18 March 2012 (UTC)

The To-do list

Tasks that are on my to-do list for this article. At the moment I do not have time to complete them, but I will next month. However, since Wikipedia is a collaborative effort and strives to be open, I felt that I should quickly jot down the things that I plan on focusing on next.

 Done I'm fairly satisfied by my choice of citations and I think I'm striking a good balance between third party positions and the details from primary sources. I've also strived to apply journal citations and reduce forum citations as much as possible. If there's problems with this during GA review or something then I'll try to fix it, but for now I think I'm doing fine. Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • Remove citations covering well-known statements. There are a few of these in the article, and they don't need a citation since they either are common knowledge or come from another article. This particularly applies to the Biomedical Significance section.
The ones I was thinking of are now  Done Jesse V. (talk) 20:40, 20 December 2011 (UTC)
  • Ensure that present-tense statements are backed by some sort of year. After further reflection and review of policy I realized that statements like "Folding@home is simulating X" should instead be better said as "In year XXXX, Folding@home simulated X" where appropriate. This way the statement stays true over the years, even when F@h has completed its work on that particular protein. Just want to make sure that such changes don't detract from readability.
 Done Jesse V. (talk) 01:51, 2 April 2012 (UTC)
  • Run this article by a few experts on the subject. I'm thankful to User:Emw for his proof-reading skills, and I'm hoping for more of the same from him or from others. Then I need to run this by one of the Folding@home experts/leaders to ensure that the article is accurate and doesn't leave out a significant statement or something. Through this process, I will essentially ensure that the article will adhere to Wikipedia policy and will also be accurate, which should make the GA nomination much easier and less stressful.
 In progress
Now  Done
Following his valued copyediting, Emw's approval
After some wording tweaks, Danno uk said that "it's looking pretty good" and "well structured and reffed, and considering the fairly dense subject maintains good readability" diff
Johnnaylor, the primary editor before I started my work, "could not find anything wrong with it" and nominated it for GA
  • Reviews from F@h scientists:
"... I took a quick look and I didn't have anything to add." - Dr. Pande
"This looks extremely well done.... On a first pass, I don't see any problems." - Dr. Bowman
  • Archive much of this Talk page. Probably every topic that has a last reply a year or more ago should go to a new page Archive 2. Discussions which have gone inactive for this long are probably obsolete and I expect no real objection to moving them to archives. I plan on doing this via the Move Procedure, outlined here: Help:Archiving a talk page#Move procedure since it seems to have the most benefits over other methods.
 Done Thanks to User:Wwood's efforts in setting up a bot to do it. Jesse V. (talk) 18:48, 16 December 2011 (UTC)
  • Remove explanations of what the WU identification numbers mean. Not only is the source of the current explanation inadequate, but there doesn't seem to be an easy definition. (citation) To avoid going into unnecessary detail and getting pretty technical, I'm electing that an explanation of this be avoided, so I will be shortly removing it.
 Done Jesse V. (talk) 20:08, 16 December 2011 (UTC)
  • Continue honing the article by removing unnecessary details or information that isn't directly supported. For example, the statement "In 2005, Pande presented results from FAH at a National Parkinson Foundation conference" is covered by a citation from the website rather than one from the NPF. We need to scan through and look for more of these. They should be either removed or covered by more appropriate citations. Hopefully this doesn't conflict too much with the "use secondary sources" idea, but if the statement is relevant it certainly needs to be backed by a source that has more information.
Pretty much  Done Jesse V. (talk) 19:42, 17 March 2012 (UTC)

I fully plan on completing these myself, but thought I'd put them out there just in case someone else wanted to chip in. Busy, Jesse V. (talk) 04:19, 7 December 2011 (UTC)

The Refinement Checklist:

  • 0 Lead  Done Jesse V. (talk) 19:48, 3 March 2012 (UTC)
  • 1 Project significance  Done Jesse V. (talk) 22:32, 15 March 2012 (UTC)
  • 2 Biomedical research  Done Jesse V. (talk) 07:15, 16 March 2012 (UTC)
  • 2.1 Alzheimer's disease  Done Jesse V. (talk) 05:58, 18 March 2012 (UTC)
  • 2.2 Huntington's disease  Done Jesse V. (talk) 06:41, 17 March 2012 (UTC)
  • 2.3 Cancer  Done Jesse V. (talk) 04:20, 1 April 2012 (UTC)
  • 2.4 Osteogenesis imperfecta  Done Jesse V. (talk) 17:48, 17 March 2012 (UTC)
  • 2.5 Viruses  Done Jesse V. (talk) 19:25, 23 March 2012 (UTC)
  • 2.6 Drug design  Done Jesse V. (talk) 01:51, 2 April 2012 (UTC)
  • 3 Participation  Done Jesse V. (talk) 18:39, 16 March 2012 (UTC)
  • 3.1 PetaFLOPS milestones  Done Jesse V. (talk) 07:58, 16 March 2012 (UTC)
  • 4 Points  Done Jesse V. (talk) 19:48, 3 March 2012 (UTC)
  • 5 Software  Done Jesse V. (talk) 22:24, 25 February 2012 (UTC)
  • 5.1 Work Units  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 5.2 Cores  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 5.3 Client  Done Jesse V. (talk) 22:24, 25 February 2012 (UTC)
  • 5.3.1 Graphics processing units  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 5.3.2 PlayStation 3  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 5.3.3 Multi-core processing client  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 5.3.4 V7  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 6 Comparison to other molecular systems  Done Jesse V. (talk) 22:11, 26 February 2012 (UTC)
  • 7 See also  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 8 External links  Done Jesse V. (talk) 20:20, 25 February 2012 (UTC)
  • 9 Notes  Done Jesse V. (talk) 05:12, 26 February 2012 (UTC)

Images

  • The logo: add a bit more border between the various elements and the edge of the image
  • V7's screenshot: update the image with the new on-screen features such as the project description
 Done Although I'll keep looking for an even better image Jesse V. (talk) 22:11, 26 February 2012 (UTC)

Other references for possible later use

So that others can see, here are my remaining browser bookmarks:

General links:

Scientific publications:

  • 2012 review: The toxic Aβ oligomer and Alzheimer's disease: an emperor in need of clothes
  • 2011 review: Protein aggregate spreading in neurodegenerative diseases: Problems and perspectives
  • 2011 review: Misfolded protein aggregates: Mechanisms, structures and potential for disease transmission
  • 2011 review: Defective Protein Folding and Aggregation as the Basis of Neurodegenerative Diseases: The Darker Aspect of Proteins
  • 2010 review: Alzheimer's Disease: A General Introduction and Pathomechanism
  • 2010 review: Converging concepts of protein folding in vitro and in vivo (focus on chaperones)
  • 2010 minireview: The role of molecular chaperones in human misfolding diseases
  • 2008 review: The Protein Folding Problem
  • 2008 review: Modeling of protein misfolding in disease. ("A short review of the results of molecular modeling of prion disease is presented in this chapter.")
  • 2008 review: Molecular and cellular aspects of protein misfolding and disease
  • 2008: The long coming of computational structural biology
  • 2008 review: Protein misfolding inside cells: The case of huntingtin and Huntington's disease
  • 2007 review: The protein folding problem: when will it be solved?

Publications from Pande et al:

  • 2010: Protein folded states are kinetic hubs
  • 2008: Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
  • 2007: Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics (for automatically improving MSM accuracy)

Not sure if some of these could go in a "Further Reading" section or something, but at least there's more information here for citations. Jesse V. (talk) 20:12, 2 April 2012 (UTC)

Regarding "this article imposes a substantial load on the reader"

In the GA review, Czarkoff mentioned that "this article imposes a substantial load on the reader". This maybe be true, there are a lot of terms and topics which are covered. Although that observation seems slightly at odds with some of the other feedback I've received, (and noted in the above "To-do List" section) this does concern me a bit. I understand this project is technical both in the software aspects and its research pursuits, and although I understand it because I wrote it, I'm afraid that it might be difficult for others. How can I make this article easier to read and more clear without backtracking from its current Good Article status? I'm open to suggestions. Jesse V. (talk) 18:07, 7 April 2012 (UTC)

To me the article is OK, as the "load" I was talking about comes from the topic itself: biochemical research, drug development, distributed computation, clustering and GPU and VGC usage for heavy computations are the topics most people known nothing about. Thus this article is deemed to be hard to read by sufficient amount of readers, as all these topics can be either explained (thus resulting in significant amount of text and mnemonic load) or "delegated" to other articles (thus making readers to navigate through the set of related articles dissolving the focus). The current text actually impressed me with the balance between the depth of coverage and ease of apprehension, as well as between medical and computing topics. I don't think something should be changed in this regard. — Dmitrij D. Czarkoff (talk) 14:03, 8 April 2012 (UTC)
Ah I see. Thanks. I was worried that the technicalities were too much of a burden, and I didn't want to scare everyone off. See I'm very impressed by this project and try to encourage others to participate (by itself a COI) but I'm also very much aware of Wikipedia's policies. A delicate balance. Glad to know that I've maintained good readability. Jesse V. (talk) 02:04, 9 April 2012 (UTC)

Comments

This is not my area of technical expertise, so I can't do a thorough check, but I did not see anything obvious. However, I was left wondering how "home" came to be part of the name. Is it referring to networking people's home computers or what? PumpkinSky talk 01:57, 17 May 2012 (UTC)

Folding@home was one of the first distributed computing projects. It's now commonplace to call these "...@home" because they are powered by volunteers running the project's program on their personal computer in their home. Of course, they can run the software at work or school, but it aims for home uses so as to reach a wider audience. Participation in these projects is crucial to their success, since every additional computer helps. There's no "networking", because my computer doesn't communicate with any other computers on the F@h network. It simply asks for some work to do from an official central server in California or in other places, receives a "work unit" which it number-crunches to its completion several hours later, and then sends it back, and repeats the cycle. This whole process is currently happening on my laptop right now, at home. Jesse V. (talk) 04:14, 17 May 2012 (UTC)

Copyediting

  • I could not quite figure out the intended meaning of this sentence, which seems to be trying to say too many things at the same time.
These results have demonstrated accuracy to observations in laboratory research, a challenge in computational biology.
Stigmatella aurantiaca (talk) 23:11, 18 May 2012 (UTC)
As I understand it, one of the challenges in computational biology is trying to make an accurate simulation which matches what you see in the lab. Often times you have to trade accuracy for speed: a low-resolution course-grained model will run very quickly but won't give you information that you might see in lab experiments, while a high-resolution fine-grained model will but it requires a lot of computations. F@h is powerful enough to run atomic-level simulations, and based on every F@h publication that I've read, they match experimental observations very well. Does this clarify things? Any ideas on how could I rephrase the statement? Jesse V. (talk) 23:23, 18 May 2012 (UTC)
You could rephrase it pretty much the way that you've just done explaining it to me. :-)
Folding@home is powerful enough to run detailed, atomic-level simulations over biologically relevant timescales. Multiple publications have verified its accuracy in matching experimental observations, which has been a major challenge in computational biology.
Stigmatella aurantiaca (talk) 04:16, 19 May 2012 (UTC)
P.S. Sorry about the word "other".
I've rephrased, clarified, and reorganized that statement and the neighboring sentences. Better? Jesse V. (talk) 06:46, 22 May 2012 (UTC)
  • Here is another sentence to work on. Like the other one, you are trying to do too many things in a single sentence. Try splitting it up.
Folding@home is dedicated to producing significant amounts of results towards protein folding, the diseases that result from protein misfolding, and novel computational methods for doing so.
Stigmatella aurantiaca (talk) 05:07, 19 May 2012 (UTC)
Split up. Jesse V. (talk) 06:46, 22 May 2012 (UTC)
  • I touched this sentence up, replacing a verb with its present participle, but what is the pronoun antecedent? (i.e. what is "them"? The results? The small molecules? Something else?)
The results may be applied to studies into the impact of specific small molecules on the process, as well as preparing them for future aggregation studies.
Stigmatella aurantiaca (talk) 05:22, 19 May 2012 (UTC)
I've rearranged the sentence:
This study helped prepare the Pande lab for future aggregation studies and for further research into the impact of specific small molecules on the aggregation process.
You seem much more fluent in the intricacies of grammar than I am, so does this address your concerns here? Could it be further improved? Jesse V. (talk) 16:37, 20 May 2012 (UTC)
Much better! Stigmatella aurantiaca (talk) 18:47, 20 May 2012 (UTC)
  • Please work on this sentence. What does the influenza hemagglutinin have to do with HIV?
In 2009, researchers used Folding@home to study hemagglutinin, a protein which is responsible for attaching HIV to its target cell by binding to certain cell surface receptors, and predict the effect certain mutations have on its binding affinity, which has implications in understanding the infection threat of a new influenza strain and the development of antiviral drugs.
Stigmatella aurantiaca (talk) 11:49, 19 May 2012 (UTC)
I'm not sure I understand your confusion. It seems clear to me that the sentence explains hemagglutinin functionality and relationship to HIV. What part don't you understand? I'd work on it for you if I knew exactly what the problem was. Jesse V. (talk) 16:37, 20 May 2012 (UTC)
  1. Hemagglutinin is a protein coded by the influenza virus genome.
  2. It enables the influenza virus to bind to sialic acid sugars on the surfaces of its target cells (epithelial cells lining the throat and lungs).
  3. The bound influenza virus is taken up by endocytosis. [1]
  4. gp41 and gp120 are proteins coded by the HIV virus genome
  5. They exploit two receptor proteins on the surface of CD4 T-cells that are normally used for cell-cell communications. gp41 binds to the one of the cytokine receptor proteins (CCR5 or CXCR4) while gp41 binds to the CD4 receptor. Not knowing that anything is wrong, the T-cell fuses with the viral envelope. [2]
Hemagglutinin, an influenza gene product, has nothing to do with HIV uptake by T-cells.
Likewise, gp41 and gp120, HIV gene products, have nothing to do with influenza uptake by epithelial cells of the respiratory system. Stigmatella aurantiaca (talk) 18:47, 20 May 2012 (UTC)
Oh. I appreciate your expert explanation. I'll put this on my to-do list of things to research and address. Thanks for bring it to my attention! Jesse V. (talk) 23:09, 20 May 2012 (UTC)
  • Discrepancy: Displayed 200 microseconds, coded 200 milliseconds in wikilink. Which?
In 2011 the Pande lab built a Markov state model from a 200-μs Anton simulation.
Stigmatella aurantiaca (talk) 06:25, 20 May 2012 (UTC)
Good catch! Microsecond. Fixed. Jesse V. (talk) 06:33, 20 May 2012 (UTC)

Good luck! Very interesting article! I hope to see it on the main page eventually! Stigmatella aurantiaca (talk) 06:59, 20 May 2012 (UTC)

Thanks! I'd like to see that as well. :) Jesse V. (talk) 16:37, 20 May 2012 (UTC)

Not "scare quotes". If you do not have quotes around the first usage, I guarantee that within a year, some helpful editor will "correct" the spelling of "Huntingtin" to "Huntington". You need some means of indicating that "Huntingtin" is the correct spelling. Stigmatella aurantiaca (talk) 07:50, 22 May 2012 (UTC)

Evidence supporting "Huntingtin" as the correct spelling:
  1. Not only the wikilink works fine, the article that it redirects to explains uses "huntingtin protein".
  2. The article cites a paper published in Journal of Molecular Biology titled "The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation"
  3. It cites another paper published in Nature is titled "Protein folding: Sticky N17 speeds huntingtin pile-up"
  4. Check out https://www.google.com/search?q=Huntingtin+protein
  5. Also see http://scholar.google.com/scholar?hl=en&q=huntingtin+protein
That all seems to indicate that "huntingtin" is the correct spelling. The article that it links to uses "Huntington disease", "Huntington gene", and "huntingtin protein". Spelling appears correct to me. Jesse V. (talk) 16:12, 22 May 2012 (UTC)
Of course it is! I'm not the person who needs convincing. What you don't want is for other people reading your article to think that you misspelled it. Stigmatella aurantiaca (talk) 16:36, 22 May 2012 (UTC)
Ah. What makes you so sure that they'll change the spelling? The fact that the wikilink works will deter most people. A regular person probably wouldn't know alternative spellings, and an expert would know that the spelling is correct. As I pointed out, the Huntington article lists the other spellings, which should educate others trying to change it. I guess I don't understand your reasoning, because I'm not convinced that someone will try to "correct" the spelling. Jesse V. (talk) 17:50, 22 May 2012 (UTC)
It doesn't have to be a well-meaning but misguided editor... although I have had experience with such in the past who messed up an article that D.H and I were actively editing at the time - see Talk:Michelson–Morley experiment#White or yellow light?. Misguided but well-meaning editors can sometimes be very persistent. See Talk:Quadratic equation#Inappropriate external link The non-specialist will have heard of Huntington's disease, but will never have heard of Huntingtin, and will very likely think that something is wrong when they see the unfamiliar term that differs by only one letter from a familiar one. Stigmatella aurantiaca (talk) 19:54, 22 May 2012 (UTC)
Ahhh! I see and understand your position now. If I was discussing the article like that, I'd probably end up defensive and make sure that thing didn't happen in other articles. Hence you're nervous that it will happen here. However, a well-meaning but misguided editor could try to change a great number of things in any article in Wikipedia. All we can do is make sure we know the correct spelling, if someone else tries to incorrectly change it, we can revert and teach them. I am prepared to do this here. I think we should leave it as it is, and there are multiple instances of someone trying to change it, then we'll see about putting quotes, a spelling-is-correct template, or some other measure in place to protect the word. With the Good Article logo in place, editors will know that someone carefully peer-reviewed it, so spelling mistakes are quite unlikely. Hence I still feel that it's unlikely that a misguided editor would try to change the spelling. Jesse V. (talk) 02:32, 23 May 2012 (UTC)
It's your decision, then. :-) It's a relatively minor issue, so I won't belabor the point. The only major issue that I have is the influenza hemagglutinin/HIV issue, which I notice that JMiall also picked up on. That one has to be fixed. Stigmatella aurantiaca (talk) 04:17, 23 May 2012 (UTC)
Don't get me wrong, I totally see where you're coming from. I'll keep it in mind and if it becomes a problem than I'll look at what you did and follow your advice. I'm working on some of the other peer-review issues at the moment, as the hemagglutinin/HIV issue requires looking at the journal citation. Since I'm outside of Utah State's network I no longer have easy access to that journal anymore. I'll have to email the librarian and try to figure out how I can access those papers from my house here in Alaska. Once I finish off some of the easier issues in the peer review, I'll look into all the ones that require research using journal subscriptions. That HIV one is top on my list. Jesse V. (talk) 05:39, 23 May 2012 (UTC)

Try these three references. I believe you have the first, but you don't have the second or third:

Kasson, Ensign & Pande (2009)
Kasson & Pande (2009)
Kasson & Pande (2008)
  1. Look up article on PubMed database [3]
  2. Free PMC article may be available. Google Scholar is also an important resource.
  3. Cite using PMID using "cite pmid" template between "ref" tags. Note how I've coded the following three citations, saving incredible amounts of typing. Clicking on the PMC sends you directly to the PMC full-text article:
  • Kasson, P. M.; Ensign, D. L.; Pande, V. S. (2009). "Combining Molecular Dynamics with Bayesian Analysis to Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin". Journal of the American Chemical Society. 131 (32): 11338–11340. doi:10.1021/ja904557w. PMC 2737089. PMID 19637916.
  • Kasson, P. M.; Pande, V. S. (2009). "Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin". Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing: 492–503. PMC 2811693. PMID 19209725.
  • Kasson, P. M.; Pande, V. S. (2008). "Structural Basis for Influence of Viral Glycans on Ligand Binding by Influenza Hemagglutinin". Biophysical Journal. 95 (7): L48–L50. doi:10.1529/biophysj.108.141507. PMC 2547437. PMID 18641068.
  1. You will usually see "Citation will be completed automatically in a few minutes. Jump the queue or expand by hand" in place of the references. Do not wait for "a few minutes" since a few minutes can be up to a day. Instead, right-click on "Jump the queue" to open up in a new tab. When the tab finishes loading, your reference will be complete.
  2. A "cite doi" template is also available. Avoid the "cite pmc" template. It's buggy. I've never used the "cite jstor" template, but it also exists. Still more are available that I haven't needed to use.
  3. About 1 percent of PMIDs and DOIs have errors, so double-check them. The second automatically generated PMID reference looks funny, but the info is correct so I'm not counting it as an error.

Stigmatella aurantiaca (talk) 09:43, 23 May 2012 (UTC)

Thanks for the information on cite pmid! Several months ago I installed the CitationBot script, which finishes the citations for me anyway. Do you think it would be a good idea to replace many of the cite journal templates in the article with cite pmid, since doing so would make it easier to edit? I just finished rewriting the statements about hemagglutinin. What do you think about it now? Jesse V. (talk) 05:50, 24 May 2012 (UTC)
You're welcome! The section reads much better. So far as replacing the cite journal templates, there is the old saying about not fixing what ain't broke. CitationBot is mostly working well for you, and there are plenty of references that don't have DOIs or PMIDs associated with them. But there are both advantages and disadvantages to the cite templates. Not being able to see the titles while you are coding is an annoyance - I have to make sure that the ref names are properly descriptive, which sometimes means long names. On the other hand, the references are generally more accurate (except for the 1% where somebody typed something wrong). I note, for instance, that your manually updated DOI, PMC and PMID for reference 78 really belong to reference 77, whereas the cite pmid template wouldn't have made such a mistake. In the end, you'll find a proper balance of when you'll use which tool for what. Stigmatella aurantiaca (talk) 09:47, 24 May 2012 (UTC)
Wow, good catch on reference 78! Fixed. Jesse V. (talk) 16:42, 24 May 2012 (UTC)

Comparing the Folding@home results against those of other labs

I'm wondering if this article could be more helpful to the reader. Though the folding@home techniques are powerful and useful, the end products of the calculations are not so easy to fix in the mind. Someone would have to read a bunch of the cited papers carefully to perceive what the results show. Our article does not supply enough detail for any one folding example to show what is at stake, and what's been accomplished.

Over the last five years a number of review articles have appeared that mention Folding@home and the work of other investigators treating the same problems. The most recent I'm aware of is: Robert B. Best (2012). "Atomistic molecular simulations of protein folding". Current Opinion in Structural Biology. 22: 52–61. We might be able to pull out one or two of the folding tasks from that review and show what the different labs have concluded. If you can get access to the paper, take a look at Figure 1. It shows the predicted versus experimental folded states for twelve proteins. At least two of these have been treated with folding@home, and perhaps more. The two that I'm aware of are labelled 'Villin' and 'WW domain' in that figure.

Finding a way to explain the Pande lab results for those two proteins would be of interest, and see how they differ from or complement the work of others on the same tasks. If others agree, I may add some relevant text. Thanks, EdJohnston (talk) 15:46, 23 June 2012 (UTC)

This is an excellent idea! I'd be happy to help as much as I can with this, and you're right, the article is somewhat lacking in this regard. Review articles are always good; they are easier to understand and they're better citation material anyway. Let's find more! I'm a student at Utah State University, but I haven't figured out how to access their journal subscriptions from outside their network. I'll work on that. At the moment, I can access the article and I see a thumbnail of the image, but I can't see a larger version of the image. Please feel free to add what you want, and I'll see if I can help explore the relevant literature where I can. Villin is mentioned here as well. Thanks so much. Jesse V. (talk) 16:16, 23 June 2012 (UTC)
You have mail. Two other reviews that look relevant are these:
  • R. O. Dror, R. M. Dirks, J. P. Grossman, X. Huafeng and D. E. Shaw (2012). "Biomolecular simulation: a computational microscope for molecular biology". Annual Review of Biophysics. 41: 429–452.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  • Harold A. Scheraga, Mey Khalili and Adam Liwo (2007). "Protein-folding dynamic: overview of molecular simulation techniques". Annual Review of Physical Chemistry. 58: 57–83. EdJohnston (talk) 16:39, 23 June 2012 (UTC)
Thanks. Like I said via email, I figured out how to access the subscription journals, so I'll take a look at those. Jesse V. (talk) 16:49, 23 June 2012 (UTC)
Here's a cool blog post on the subject: [4] Jesse V. (talk) 16:49, 25 June 2012 (UTC)
I also found two papers that might be useful: The Fast and the Slow: Folding and Trapping of λ6–85 and Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW. They also talk about MSM technology, so they are good citation material as well. Jesse V. (talk) 06:59, 27 June 2012 (UTC)

The to-do list

To anyone who is also interested in editing this article, here is the to-do list:

  • These questions ought to be answered:
  • How are the local minima in the energy landscape from which the simulations are started found? Why is this not computationally difficult?
  • How do you know that the simulation will reach a minima, and how is the simulation direction chosen?
  • In what way do MSM's explore the protein's phase space differently than normal simulation techniques which don't avoid simulating the "waiting" inside the energy minima?
  • Is this approach adequate for exploring the protein's phase space? If it does such a thorough job and gives you so much conformation and kinetic information why are really long simulations so important?
  • Does F@h simulate further after a protein has arrived at its folded shape, and how does that work with MSMs?
  • And there needs to be more information about comparing F@h results to experiments, as described in the above section.

I don't believe that I have the technical knowledge to answer these by myself, but I'm very willing to support anyone who wants to pursue them and I'd welcome assistance. The publication Everything you wanted to know about Markov State Models but were afraid to ask may be helpful. • Jesse V.(talk) 23:49, 17 August 2012 (UTC)

Actually, this new FAQ answers most of these questions: http://folding.stanford.edu/English/FAQ-Simulation • Jesse V.(talk) 16:07, 10 September 2012 (UTC)
And now I know the answers to the rest. I'm not convinced that it would be appropriate to answer all of these questions in the article though, but most of them are there. • Jesse V.(talk) 15:49, 14 September 2012 (UTC)

any hard-core results yet?

article says some of the virtual findings were being pursued in labs, etc. but the statements appear to be several years old. — Preceding unsigned comment added by 75.84.95.229 (talk) 10:58, 25 December 2012 (UTC)

The papers for those older results are out and the references are reliable and backed up by third parties. That's why the article uses them, but there's hard results discussed in the article. The newest findings have not been completely verified and so there's a bit of speculation and hope around them, just as there is with many other scientific discoveries. It's not appropriate to put speculation in Wikipedia articles, unless such speculation comes from third-parties, which it didn't. I keep a close eye on folding.typepad.com, and I'll do my best to promptly add any solid verified results into the article. • Jesse V.(talk) 20:31, 25 December 2012 (UTC)

ok thanks jessev. will be interesting the day when a human application actually happens. — Preceding unsigned comment added by 75.84.95.229 (talk) 20:36, 28 December 2012 (UTC)

Stanford and Bay Area

I had added this article to the WP:San Francisco Bay Area task force, and categorized it as Category:Science and technology in the San Francisco Bay Area. these were removed, the reason being that folding at home has nothing to do with the bay area. However, since its based at Stanford, i would argue it does, as stanford is in the area. If consensus is that university web-centric projects are not considered to be part of the geographical region the university is located in, i will concede the point and move on. however, if a consensus of editors here think it should be categorized as connected to the bay area (remember, it can have low priority/importance to the area, doesnt have to mean its strongly associated with it), we should add it back. I added it to the Portal:San Francisco Bay Area, so i need to know if i should remove it. ps excellent work on an important article.Mercurywoodrose (talk) 03:01, 8 March 2013 (UTC)

I understand your point. Folding@home started in Stanford, but as you can see from this page, there are server centers in many other places across the world. I looked up a few IPs and found University of Virginia, Rensselaer Polytechnic Institute in New York, and Hong Kong, but many of them are in Stanford. The contributors to the project come from across the world. There's is an argument that because it started in Stanford that it belongs in the Bay area, but it's not a local or confined science and technology, so in my mind there's a stronger argument that it has very little to do with the Bay area. It'd be more appropriately tied to Stanford than the Bay. That's my vote. And thanks, Mercurywoodrose. :) • Jesse V.(talk) 03:25, 8 March 2013 (UTC)
Thanks, I wasnt entirely clear how distributed the folding@home endeavor was. My inclination is to have it in the CALI/SFBA project, but I still consider myself new to the whole project arena, and I do wonder what the precise inclusion criteria are for projects. For my part, i wont return it to the project, esp. since, well, its not that big a deal. articles are the key thing. And, if someone ever wants to distro a DVD of various topics, they may be adding CALI articles to the US project articles (along with other states with their own projects), or even Stanford to the CALI project for inclusiveness. i asked about that elsewhere, didnt get an answer.Mercurywoodrose (talk) 20:10, 17 March 2013 (UTC)

References

Currently, the article has 194 references and probably over 250 individual citations, with many sentences having 2-3 citations each. For example in the "client" section the last portion of the sentence "the client itself is proprietary for security and scientific integrity reasons" has 3 citations. I'd imagine this is somewhat excessive. Unless the sentence has multiple facts within or is likely to be challenged there is really only a need for a single citation. I'm not an expert in this particular topic so I'd rather not take the task of cutting out redundant citations (for risk of taking out something important), but I do think it needs to be done. Coinmanj (talk) 00:42, 19 June 2013 (UTC)

One of the main problems was that the information was a bit scattered, and it was only through the combination of multiple sources that one could definitely back up a lot of the statements. I'll double-check the citations though and see what, if anything, can be done. • Jesse V.(talk) 00:47, 20 June 2013 (UTC)

All-atom simulation of water

The "Cancer" section mentions an "all-atom simulation of water", linked to Water model. Is this the same as a 3-site model, or some other specific model discussed in that article? If someone knows, can they link the term to the relevant section of the "Water model" article? Thanks. - dcljr (talk) 19:38, 1 November 2012 (UTC)

Sorry, I've been offline a while. I emailed Dr. Pande to ask. He said TIP3P. I'll ask Jesse to make the update. 7im (talk) 22:45, 13 September 2013 (UTC)

"Most powerful molecular dynamics simulator"

Resolved

The introduction mentions that Folding@home "is the world's most powerful molecular dynamics simulator", but I don't see a citation for that claim anywhere in the body (nor do I see that specific claim mentioned or expanded upon in the body, which it should be if it's important enough to include in the lead). Given that the Blue Gene supercomputers do protein folding calculations and the latest iteration of Blue Gene -- Blue Gene/Q -- runs over two times faster than Folding@home, I think that claim needs a citation. Emw (talk) 11:57, 26 October 2012 (UTC)

I'll see about fixing this. Further expansion is in the paragraph on Anton. • Jesse V.(talk) 14:35, 26 October 2012 (UTC)
Should be fixed now. Thanks for the catch. • Jesse V.(talk) 18:01, 26 October 2012 (UTC)
The revised sentence "In October 2011 the project was the world's most powerful molecular dynamics simulator" is slightly better, but I think it's still problematic:
  • The citation backing the claim is a blog post from the director of Folding@home. Even if they're correct, claims of the form "X is the favorable superlative Y in the world" need an independent source to be reliable.
  • The available data in File:Folding@home_and_Supercomputer_Computational_Powers.png makes the claim tenuous, or a bit persnickety. It's tenuous because the data shows Folding@home's performance as dipping from June 2011 through November 2011, below that of the supercomputer with a data point in June 2011. What was the name of that supercomputer? Did it do molecular dynamics? Even if that unknown supercomputer did not do MD, the K Computer supercomputer did. Upon its release in November 2011, a month after the date the claim in question was made, K Computer was more powerful than Folding@home.
A statement like "The project was the world's most powerful molecular dynamics simulator until mid 2011" would be more straightforward, in my opinion. It would also be unambiguously supported by the available data. Even then, though, I think such a claim still warrants further search for a reliable source. Emw (talk) 13:32, 27 October 2012 (UTC)
  • You might want to refresh the page or something, because I added a reference to a journal citation. Look at citation 140, published October 2011. The paragraph on F@h follows a paragraph on Anton. Here's the relevant sentence: To date, this distributed computing project comprises over 100,000 processors volunteered over the internet, making it the largest single contemporary computational resource dedicated solely to the simulation of bio-molecular systems, capable of exploring dynamic processes occurring over time-scales of milliseconds and providing estimates of both equilibrium properties and, in some cases, kinetic rates.[10] (with 10 being a reference to Bowman's, Voelz's, and Pande's Taming the complexity of protein folding paper).
  • Looking at http://i.top500.org/system/10810, I see that the K computer was #1 in June 2011 at 8.162 petaFLOPS, and still #1 in November 2011 after being upgraded to run at 10.510 petaFLOPS. When I turn to the citations in the K computer article, I see this website, published June 2011, which reads Use of the K computer is expected to have a groundbreaking impact in fields ranging from global climate research, meteorology, disaster prevention, and medicine. So it's not focused on molecular dynamics, but I have found a few results that indicate that it can do them (example). Up till now, I didn't know the K computer could do that. If it fired up any molecular dynamics software at all, and under the assumption that said software scaled well and ran at the performance that the LINPACK benchmark reported, then it would be faster than F@h. I think it's safer to assume that events happened this way, so I'm adjusting the sentence as you suggest. (although isn't there supposed to be a dash in between "mid" and "2011"? I added one; I think it looks better that way) • Jesse V.(talk) 15:05, 27 October 2012 (UTC)
Thanks for noting the excerpt from the referenced journal article in citation 140 -- the article is paywalled, so I didn't see that part. I don't think the excerpt supports the sentence in question. The authors say Folding@home is "the largest" system (i.e., most processors), while the sentence in question says it's "the most powerful" (i.e., most FLOPS). As the graphs in File:Folding@home_participation_per_client.png and File:Folding@home_and_Supercomputer_Computational_Powers.png show, the number of active processors ("largeness") and FLOPS ("power") are different things and aren't necessarily correlated. The qualifier "dedicated solely" used by the authors is also significant, which I think we likely agree on from my reading of your paragraph about K computer above. Emw (talk) 18:38, 27 October 2012 (UTC)
Your welcome. Sometimes its not clear to me if Utah State gave me access or if the actual publication was open. No harm in noting the excerpt, it's convenient to you in either case. You raise a good point; if I remove the reference in the Comparison section, does that change anything and do I need to do anything else to solve this whole issue? • Jesse V.(talk) 18:52, 27 October 2012 (UTC)
I think removing reference 140 would be enough. Emw (talk) 19:13, 27 October 2012 (UTC)
 Done • Jesse V.(talk) 06:44, 28 October 2012 (UTC)


I'm not seeking to reopen the above discussion, but on a related note: The article currently says "The project was also the world's most powerful molecular dynamics simulator until mid-2011." Since this is apparently based on the performance section, shouldn't we clarify that Folding@Home was faster than every other system, not just other molecular dynamics simulators? For example: "It was also the world's most powerful computing system from early 2007 through mid-2011." Or, if we don't want to group it with supercomputers, we could say "The system was also more powerful than the world's fastest supercomputers from early 2007 through mid-2011." Thoughts?Proxyma (talk) 01:05, 7 October 2013 (UTC)

updated Performance graph needed

If anybody (Jesse V.?)has a template (PSD?) for the Performance graph, it might make sense to update again. Current performance is much higher than in the graph, which was last updated April 2012. Currently Native TFlops = 9377 and x86 TFlops = 18554. Proxyma (talk) 01:09, 7 October 2013 (UTC)

Yes, good call on that. That data came from a Google Spreadsheet which is still being maintained and updated. The whole article needs a refresh, since FAH has changed a bit in the last year or so. I'll work on that when I have some time. • Jesse V.(talk) 02:45, 7 October 2013 (UTC)
Cool. What other changes are you referring to? I've noticed the new website and also expanding beyond Stanford (Memorial Sloan-Kettering). Proxyma (talk) 04:30, 7 October 2013 (UTC)
I'd like to double-check if there have been any new publications or other scientific accomplishments, and then possibly mention them in the article. Also, FahCore 17 uses OpenCL and runs in Linux natively, so there's that. 7.3.6 also provides a new interface and some new features. And those changes you mentioned. • Jesse V.(talk) 18:58, 7 October 2013 (UTC)

article size

this user is calling upon the community to check into the article and split sections accordingly while removing content which are not necessaryFAMASFREENODE (talk) 17:28, 12 June 2016 (UTC)

I disagree with this tag. This is a Featured Article and I see no mention of length in the GA review, the peer review, or the FA reviews. If you compare the article from the FA promotion to now, you can see that the article has not significantly expanded and there have been no major changes. There are many different aspects of Folding@home and the article should cover them all to be thorough. It's also worth noting that List of Folding@home cores was split off long ago, which significantly shortened the article. I think the prose and flow is fine and I suggest that editors remove the tag. 216.249.95.134 (talk) 14:28, 24 June 2016 (UTC)

1000 teraflops is not 1 petaflop?

This appears to be some sort of bad faith RfC, feel free to re-open if you're confident that it is not, otherwise I'm hoping to save some people a waste of time SemanticMantis (talk) 16:35, 10 November 2016 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

foldingforum.org post shows the project reaching 100000 teraflops in may 2016. is it not 100 petaflops?Minimobiler (talk) 18:42, 29 October 2016 (UTC)

What is your question about the article? The lead states 100 petaFlops. CuriousMind01 (talk) 13:22, 8 November 2016 (UTC)

1000 teraflops is 1 petaflop. I see no evidence that anyone thinks otherwise. Why is this an RfC? Maproom (talk) 07:40, 9 November 2016 (UTC)

I see that Minimobiler is now blocked for edit warring. Maproom (talk) 08:33, 9 November 2016 (UTC)
The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

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On proprietary software license as a means to guarantee scientific integrity

An anonymous editor (or several) have kept removing a paragraph about critiquing the use of closed-source client software as the means for preserving security and scientific integrity as proposed in the article.

The removal of the paragraph doubting this rationale, including the latest iteration, cites "original research" as the reason, while in fact all the statements in that critique are supported by references.

Needless to say, the openness of the scientific methodology of the research extends to the design and workings of the software tools used to process data.

The critique of this approach is not intended as a means to undermine the integrity of this project, but rather to balance a view presented by a scientific project as if it were a matter-of-fact, when in fact it is not.

I have restored an enhanced version of that critique, with better explanation of how the current client software already has functionality that can preserve integrity of the work even if it were opensource, as to avoid the possibility of unintentional implication of non-integriy, if it were the motive for removing the critique by those who could be associates of the research project.

I hope that a well-balanced section on this matter can be reached.

--A. Gharbeia (talk) 11:36, 26 December 2017 (UTC)

FAR prep

Noticed that there are two cleanup tags on this article. One being all the way back in 2016. Between this and non-sourced material in here, I think an FAR is in order. GamerPro64 04:38, 6 November 2019 (UTC)

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