Talk:Rosetta@home

User comment

Great work, really. -Tribaal 08:29, 13 April 2006 (UTC)

Public or Private Results

I can't seem to find, and would love to see, a section on this page about who "owns" the results to the computations. It's a point of contention I have with all these projects. I'd feel like a chump if I was the one to contribute the results that led to some big-pharma corporate to patent the only cure to some disease. The results of these DC projects should be "open sourced" so to speak, shouldn't they? I think a disclosure of this information would be a useful part of this article.

This page reads like an ad

Someone did a lot of work expanding this page with tons of new information. However, currently the page is written like an ad for how great Rosetta@home is. This part sounds like a solicitation for donations: "Decoding the human genome may be the greatest scientific achievement of this century. But before that knowledge can be used, scientists need to take the research a step further — they need to understand the proteins that are built from our DNA. Proteins are the parts that make up the machinery of living cells." Or this: "By participating in the Rosetta@home Project, volunteers help verify and develop these revolutionary new algorithms." Ww.ellis 12:11, 10 May 2007 (UTC)

• Both items have been taken care of. I removed the paragraph containing the first issue ("Decoding the human genome...") because it was mostly redundant with the paragraph below it. After that, "revolutionary new algorithms" was changed to "new protein structure prediction algorithms". Emw2012 (talk) 01:13, 1 July 2008 (UTC)

Wikipedia is not a how-to guide

I actually used the "How to join" section to install Rosetta@home on this computer. However, articles aren't supposed to read like instruction guides. Could any user suggest a way to rewrite that section to conform to style guidelines? --Grace 07:40, 3 June 2006 (UTC)

Agreed. The 'how to join' section is not appropriate. Perhaps just a link to the project's how-to page would be acceptable. 129.64.68.20 19:44, 3 June 2006 (UTC)

From my perspective (having written most of this page), the goal was to allow the Wikipedia reader to find the needed information as painlessly as possible. As the first poster said, he/she installed it per the instructions in Wikipedia. As long as it helps people, I don't see why it can't be kept. So, let it be for the moment please, thx. Dhatz 20:58, 3 June 2006 (UTC)

Good work writing the page, but the section does need to be rewritten according to Wikipedia policy. Rather than the imperative "Install the program like this", it needs to have the descriptive tone of "This is how the program is used" - or it could be replaced with a link to the project's how to page as the second commenter said. --Grace 08:04, 4 June 2006 (UTC)

OK, could you point me to that Wikipedia policy? Also, which link to the project's how to page do you suggest to use instead (specific URL please)? Btw the prior poster didn't suggest, he simply DELETED the entire section. Dhatz 17:32, 4 June 2006 (UTC)

WP:NOT is a good start. On a sidenote, I think the 'how to join' section is ok, only needs a little editing.-- _{Piotr Konieczny aka Prokonsul Piotrus  talk}  16:55, 25 July 2006 (UTC)

Copyright violation?

I've noticed that this page uses large amounts of verbatim text from other websites: is the Wikipedia copyright policy being followed here? (Specifically, read section 4 - "Contributors' rights and obligations".) Mike Peel 10:30, 4 June 2006 (UTC)

Please be specific about which sections you mean. Any verbatim text is quoted (with quote marks), indented, has a link to the original source at the end and has been copied over with permission. Dhatz 17:19, 4 June 2006 (UTC)

I was referring to many parts of the page - basically every section which quotes more than a sentance from an external source. So long as the verbatim text has been copied over with permission from those with the copyright, then I don't think there's a problem. Mike Peel 19:43, 4 June 2006 (UTC)

Although it would be best if the Rosetta@home project would licence their contents under GFDL or CC or some other copyleft licence we could use.-- _{Piotr Konieczny aka Prokonsul Piotrus  talk}  16:55, 25 July 2006 (UTC)

As an example, consider list items 1-3 in the 'Medical Relevance' section, which are taken verbatim from http://boinc.bakerlab.org/rosetta/rah_medical_relevance.php and not put in quotation marks. While the author (David Baker) is probably fine with having that content mirrored on Wikipedia, "Copyright © 2008 University of Washington" is clearly visible on the bottom of the page. The use of second-person should be fixed at the very least. Emw2012 (talk) 05:42, 1 July 2008 (UTC)

Project Signifigance could do with some rewording.

ie. "Decoding the human genome may be the greatest scientific achievement of this century. But before we can...", sentances starting with "But". --FauxFaux 15:49, 25 October 2006 (UTC)

Suggestions

I suggest you should have a references section at the end of this article. Many of your statements have inline web-links which could readily be turned into references using {{tl:cite web}} or straight out <ref></ref> statements. Also: don't put links in the middle of sentences put them at the end. Reading the automated peer review will provide links to the relevant policies / preferences.Garrie 03:01, 19 January 2007 (UTC)

Human proteome has ~400,000 proteins?

The human proteome has ~400,000 proteins and there are more proteins in other organisms. Where you guys got 400k number from? It is less then 30k genes in in every given human being. So total number of significant proteins would be also less then 30 000. Even given that one gene can code for more then one protein it still would not make any difference since those genes relatively rare. On the other hand you can count human population as a whole counting every mutation as separate protein, this way you will end up having millions of proteins. But those one not a big deal since there shape would be very close to resolved ones and predicting shape from scratch, from amino acid sequence computationally will yield more errors in predicted shapes. The other possibility - count antibodies generated by human immune system would also give you millions of possible proteins. But those luck any sequence, so Rosetta could not help with them.

This number - 400k for me sounds like a lie, simply made to justify project. 204.16.188.3 03:22, 13 March 2007 (UTC)

• http://en.wikipedia.org/wiki/Proteomics - >500k ? "In humans there are about 25 000 identified genes but an estimated >500 000 proteins that are derived from these genes." --82.152.213.208 20:08, 5 September 2007 (UTC)
  • In reality, there is billions of possible proteins that any given human body can produce. Check antibody article for example. But only ~25k proteins is fully hardcoded in a DNA. So, when you talking to public it is more of a matter what you want to emphasize - you technically will not lie saying almost anything giving careful selection of words. And, to complicate matter, there is way more than just proteins that define how our body is developing. RNA enzymes, or ribozymes and sugars are another examples. TestPilot 21:22, 1 May 2008 (UTC)

• Because of discoveries in alternative splicing and (as TestPilot alluded to) class switching, it's pretty widely accepted that there are far more proteins than there are genes. And because comparing that vague number (> 20,000-25,000 possible human protein sequences) to the number of solved structure in the PDB (< 48,000) doesn't convey the magnitude of the sequence-structure disparity, I removed the reference to the number of possible human proteins altogether. The new reference, to the number of protein sequences in the non-redundant protein sequence database (> 6,600,000), also reflects the problem better (all organisms' sequences : all organisms' structures) without the implied false analogy (all human sequences : all organisms' structures). Emw2012 (talk) 22:39, 30 June 2008 (UTC)

'Baker lab' section: nomination for deletion

The Baker lab section is outdated (compare the post-docs listed there to those listed at the referenced link). It seems inappropriate to list the ~20 post-doctoral fellows now at the Baker lab (with that number likely increasing). Considering that the only other information in that section is that the lab is at the University Washington and that David Baker runs it (plus department and HHMI information seen in other places in the article), I'm nominating the section for deletion. The information can easily be incorporated into the introduction, which, according to the archived peer review, should be expanded anyways. Emw2012 (talk) 17:51, 30 June 2008 (UTC)

After a little over a week without any objection, I just deleted the 'Baker lab' section. Instead of moving the information to the introduction, I thought it'd be more appropriate to put it into the article on David Baker. Emw2012 (talk) 05:32, 8 July 2008 (UTC)

Differences between protein research projects

This section is great! It concisely explains the difference between the two programs without getting into too much detail, which I think is great for newbies like me. It would be nice to expand this section to discuss which diseases are more relevant to each project, so that people know which diseases they are fighting when they join the project. Mad props to whomever made this section! 76.190.151.109 (talk) 04:11, 3 July 2008 (UTC)

This article should be thoroughly referenced

If the project is as notable as it claims it should be easy to find proper references to back it up. Otherwise it it self-contradictory. A lot of the science stuff does not belong in an article about the project but rather in the science articles related to the topics discussed. This is an encyclopedia. If people contribute they should do it in the right place.. 81.98.244.47 (talk) 00:11, 5 July 2008 (UTC)

Just to make it clear I'm not in favour of the material being deleted, but just that the science be moved to a separate article.. 81.98.244.47 (talk) 00:13, 5 July 2008 (UTC)

I agree that the article should be more referenced, and that a lot of the information is in the wrong place. While I also agree that the article reads like an ad (in response to your tag), the statement that "it is without ANY references" is obviously false. There are seven references and multiple sources that haven't been converted into references yet. Compared to the Einstein@home, SETI@home and Climateprediction.net articles that's not notably below average.

The bigger issue is that the article pushes Rosetta@home. None of the BOINC projects' articles have anything like a 'Joining the project' section, which is basically a combination of a 'how to' and an ad. Until someone has a good reason to include that section, making Rosetta@home unique among the BOINC projects (and installable software in general), I'm going to replace it with a link as previously suggested. I'll also work on getting sections to NPOV.

In regard to relocating most of the science talk to articles, I think the other distributed computing articles are a good yardstick on how much of it should be included. —Preceding unsigned comment added by Emw2012 (talk

You're right that there are some references, but most if not all of the actually project-related content is unreferenced. I agree with everything else you said. 81.98.244.47 (talk) 09:12, 7 July 2008 (UTC)

After adding about 30 references since my last comment and doing major rewrites of most sections of the article with specific attention to NPOV/non-ad, I think it's safe to remove the advert tag. Let me know of any further revision you think necessary.Emw2012 (talk) 05:45, 11 July 2008 (UTC)

I agree Emw2012, you've done a very good job improving this article and I'm happy to see the tag removed. 81.98.244.47 (talk) 20:14, 11 July 2008 (UTC)

GA Review

This review is transcluded from Talk:Rosetta@home/GA1. The edit link for this section can be used to add comments to the review.

Hi, I will be reviewing this article for GA. The article seems to be very well written. However, there are a few problems I notice. —Mattisse (Talk) 18:20, 5 September 2008 (UTC)

• Per WP:EL there are not supposed to be any external links in the article. This article has quite a few. These need to be converted into citations using a consistent format.

• Done. Emw2012 (talk) 00:52, 7 September 2008 (UTC)

• Is this a reliable source: http://boinc.bakerlab.org/rosetta/forum_thread.php?id=2431&nowrap=true#40756? It seems to be a messageboard or a forum.

• While forums are typically unacceptable sources, I've decided to include posts from Rosetta@home scientists and moderators because they offer reliable information that doesn't seem to be available elsewhere. Emw2012 (talk) 00:52, 7 September 2008 (UTC)

• This paragraph is a little confusing:

In early 2008, Rosetta was used to computationally design a protein with a function never before observed in nature.[20] This was inspired in part by the retraction of a high-profile paper from 2004 which originally described the computational design of a protein with improved enzymatic activity compared to its natural form.[21] The research paper, which cited Rosetta@home for the computational resources it made available, represented an important proof of concept for this protein design method, and could have future applications in drug discovery, green chemistry, and bioremediation.

• Does the "research paper, which cited Rosetta@home for the computational resources it made available" refer to the high-profile paper from 2004 that was retracted?

• I've attempted to clarify the usage -- thanks for pointing that out. The fix should take care of this point and the preceding one. Emw2012 (talk) 00:52, 7 September 2008 (UTC)

• "Rosetta made history by being the first to produce a close to atomic level resolution, ab initio prediction in its submitted model for CASP target T0281." This statement appears not to be cited.

• Reference added (see Figure 3 in linked site). Emw2012 (talk) 05:58, 8 September 2008 (UTC)

• The section Folding@home does not have any citations.

• References added. Emw2012 (talk) 05:58, 8 September 2008 (UTC)

• You have done an excellent work on this article. One more thing, if possible, I notice that you use cite xxx for almost all references but a few you did not format that way and they do not have access dates. References should be consistently formatted. —Mattisse (Talk) 22:49, 7 September 2008 (UTC)

• I've gone through and added accessdate attributes and values for all usages of 'cite web'. I've refrained from using them on 'cite journal' references, since scientific publications are so rarely altered. While this is consistent within a particular type of reference, let me know if adding access dates for all references is preferable. If so, then I'll go through and add them. Emw2012 (talk) 05:58, 8 September 2008 (UTC)

Using the 'cite journal' is fine. —Mattisse (Talk) 15:06, 8 September 2008 (UTC)

• Not sure why, under Development history and branches the "</ref>" is showing up at the end of the second sentence.

Nevermind! I found it. —Mattisse (Talk) 15:28, 8 September 2008 (UTC)

• You still have an external link in the image caption: "Superposition of Rosetta-designed model (red) for TOP7 onto its x-ray crystal structure (blue, PDB ID:".

• Removed. Emw2012 (talk) 15:34, 8 September 2008 (UTC)

It's still there: http://www.rcsb.org/pdb/files/1qys.pdb in the caption.

Sorry about that. Both that EL and the EL to Rosetta Commons in the infobox have been fixed. Emw2012 (talk) 15:59, 8 September 2008 (UTC)

• I fixed a few little things, like numbers under 10 are to be spelled out. Great job on the article! —Mattisse (Talk) 16:02, 8 September 2008 (UTC)

Final GA review (see here for criteria)

1. It is reasonably well written.

   a (prose): b (MoS):

2. It is factually accurate and verifiable.

   a (references): b (citations to reliable sources): c (OR):

3. It is broad in its coverage.

   a (major aspects): b (focused):

4. It follows the neutral point of view policy.

   Fair representation without bias:

5. It is stable.

   No edit wars etc.:

6. It is illustrated by images, where possible and appropriate.

   a (images are tagged and non-free images have fair use rationales): b (appropriate use with suitable captions):

7. Overall:

   Pass/Fail:

Comment

A major improvement would be if you explained why predicting protein structures ab initio is difficult and why this task requires so much computing power. This would be a summary of the protein structure prediction article. Tim Vickers (talk) 02:45, 12 September 2008 (UTC)

I added information on ab initio modeling to the third paragraph of the Project significance section. Thank you for the input. Emw2012 (talk) 04:58, 28 September 2008 (UTC)

Great

This is very, very cool. Keep up the excellent work.69.122.62.231 (talk) 03:05, 1 December 2008 (UTC)

Dumb Question

I was under the impression that pages linked directly to the front page, in particular featured articles, were traditionally protected for the duration of their display. This is clearly not the case here. What gives? Am I completely off base, or did somebody screw up the system? 75.148.127.194 (talk) 01:56, 1 December 2008 (UTC)

• My understanding is that most of "Today's featured article"s retain their normal level of protection, except that move-protection is added in cases where it was not previously applied. This policy, which seems to extend back at least a few months, has been used in this TFA as it has been in others. Emw2012 (talk) 05:35, 1 December 2008 (UTC)

Not a Top-notch Article

This may be an important topic, but this article is not of the quality for a featured article. There are many problems both in the aesthetics of mussed-up links and errant wikicode, as well as a lack of depth. Just a comment.TeamZissou (talk) 20:03, 1 December 2008 (UTC)

• Could you be more specific? Which links are disordered, and which pieces of wikicode need fixing? According to a checklinks assessment of this article, all of the links in the 'References' section seem fine. The 'External links' section seems alright too. Could you also please mention which sections you find to be lacking in depth, and how so? Any other specific suggestions would be greatly appreciated. Thanks in advance. http://en.wikipedia.org/w/index.php?title=Talk:Rosetta@home&action=edit&section=14 Emw2012 (talk) 19:09, 3 December 2008 (UTC)

Wow. I'm not sure what happened, but the current article seems to qualify for a featured article. When I looked at the article on Dec. 1st, I saw sparse information and many broken citation and web links -- it looked like a neglected "B" class article. I can't explain the difference, but apparently I was looking at a different version or something was wrong on my end... Who knows?! My apologies and thanks for building the current article. TeamZissou (talk) 20:03, 3 December 2008 (UTC)

I agree that this article is not as top-notch as I would expect. There are significant portions of text that, while probably true, are not covered by citations so I mentally call them into question. I thought a featured article had "comprehensive" coverage, but this article seems surprisingly short. Also, there seems to be a lot of technical information, especially in "Project Significance", and its not clear what exactly everything means. I look at other featured articles and they are significantly different. I even looked at the article when it was nominated and it seems to have the same issues. Perhaps I am missing some policy, but at the moment I am disputing/questioning the featured article status. Also, to those that are passionate about Rosetta@home, using simple terms to explain complex things, and providing more details about the project makes a better encyclopedic-advertisement anyway. :) Jessemv (talk) 15:42, 22 September 2011 (UTC)

Sorry for the delayed response, I'm just noticing this now. First, I think the post above makes a few points worth addressing. For reference, this was the version of the article when the concerns immediately above were expressed.

• There are significant portions of text that, while probably true, are not covered by citations so I mentally call them into question.

I count two paragraphs without citations out of about 34 paragraphs in the body of this article. The first paragraph is in 'Computing platforms', beginning "Like all BOINC projects, Rosetta@home runs in the background of the user's computer". The second paragraph is the one that begins the 'Project significance' section. While a citation might benefit these paragraphs, I don't think either contains statements that are contentious, exceptional, or likely to be challenged -- which are generally the conditions under which citations are required. WP:When to cite and WP:LIKELY are two helpful supplements to WP:FACR 1c to consider here. Like most other featured articles, citations in this article often cover statements made in several sentences within a given paragraph

• "I thought a featured article had "comprehensive" coverage, but this article seems surprisingly short."

This article contains about 3600 words of readable prose as measured by this tool, and includes 86 citations. Among featured science articles of mid-to-low importance, this is actually slightly longer and more heavily cited than normal.

• "Also, there seems to be a lot of technical information, especially in "Project Significance", and its not clear what exactly everything means."

In articles about scientific and technical subjects it's always difficult to gauge what the appropriate level of depth is. I think this article contains about the same degree of depth and technical information as featured articles on Virus and DNA. I think that section makes a reasonable trade-off between flow of writing and explaining for the layperson technical jargon via appositives, context, wikilinks and such. A high-level summary of the project's significance without a significant amount of technical information is given in the article's introduction.

Second, I think it should be noted that the editor who originally posted concerns about this article retracted those concerns because they were apparently viewing some version of the article that was drastically different than the one that actually existed at the time. Saying that one "agrees" with a statement immediately below the retraction of that statement seems like a poor word choice at best, if not also a bit disingenuous. Emw (talk) 19:36, 5 November 2011 (UTC)

Yes. I agree with your statements Emw, and I retract my agreement. Working on the Folding@home article has been an educational experience, both about the subject itself but more relevantly about Wikipedia policies. I see now that the Rosetta@home article does in fact follow Wikipedia policies. In particular I was referring to a lack of citation in the lead, and I had assumed that the "need citations to cover statements" policies don't apply there as much. In light of this and other Wikipedia policies, I take back my agreement. It still seems that the article is technical, but I guess that's difficult to avoid for comprehensive coverage and "brilliant" writing. To sum up, it was wrong of me to agree because I didn't know policies enough, and so I stand corrected. Thanks. Jessemv (talk) 19:50, 5 November 2011 (UTC)

Effects of WP main page exposure?

If the project had 77 teraflops worth of processing power on 30 nov, how much does it have now, having been exposed on one of the most visited pages on the internet? Would be fun to know... EditorInTheRye (talk) 13:16, 7 December 2008 (UTC)

• There was a boost in the number of new users joining the project for about two days (see here), but no substantial increase in overall processing power. The project's main site happened to be experiencing trouble for about the first half of the UTC day, and seemed swamped with requests when it eventually came back up. The article got 26.8 thousand fews the day it was featured, 8.4K the next day, then 5.7K, 4.7K, 543, and 252 (yesterday) (see [article traffic statistics for Rosetta@home in December 2008]). That was in addition to 7.2 million views of the Main Page on December 1 2008. I imagine that the inopportune timing of having the main project site down and bogged thereafter was the main factor in the insignificant boost in processing power and active users. As the primary author of the article, it would have been nice to know that the R@H article was going to be 'Today's featured article' at least a few days in advance. Instead there was no mention on the article's Talk page or mine beforehand, nor much advance notice in the TFA archives. I learned by seeing it on the main page, which, while a great surprise, didn't give me time to notify the Rosetta@home team that they should prepare for a large increase in server demand. Emw2012 (talk) 16:20, 7 December 2008 (UTC)

Rosetta Beta as opposed to Rosetta Mini

I think that this article could benefit from a section explaining exactly what the differences are between the Rosetta Beta and Rosetta Mini applications. —Preceding unsigned comment added by Bawkbawkboo829 (talk • contribs) 03:45, 28 July 2010 (UTC)

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Confuses the distributed computing project with the underlying software

Rosetta@Home seems to be so called because it is based on the Rosetta software, but there is no actual page for that software, even though it is referenced from at least one other article. (It is not hyperlinked in either.)

David Woolley (talk) 11:02, 12 April 2020 (UTC)

FA in need of review

This is a 2008 promotion that is in need of a review against current FA standards. The article seems overly reliant on primary sources, with way too many citations to sources too closely associated with the subject, such as Rosetta@home, Boinc, David Baker (Baker D) and Brian Kuhlman. There is also a number of citations to users' posts in forums, which don't seem to meet WP:RS. The article is in need of citations in many places; I will flag some of them with the cn tag. RetiredDuke (talk) 17:47, 8 August 2020 (UTC)

Blocked sock. JoJo Anthrax (talk) 13:46, 31 October 2022 (UTC)
The following discussion has been closed. Please do not modify it.
This reads like a promotional piece This article is heavily promotional, reads like an add put forth by people with a strong COI. And the reader should be cautioned that the problem of protein structure prediction, the main thrust of Rosetta@home, has been already solved using artificial intelligence by DeepMind, a company owned by Google! DeepMind developed the predictive tool AlphaFold that incorporates Rosetta input among many others to make their most accurate predictions of protein structure. AlphaFold has overtaken Rosetta in the CASP (Critical Assessment of protein Structure Prediction) competitions. TruchaForelle (talk) 23:48, 5 October 2022 (UTC)

References