Wikipedia:Peer review/Rosetta@home/archive3

Rosetta@home

 * Previous peer review
 * A script has been used to generate a semi-automated review of the article for issues relating to grammar and house style; it can be found on the automated peer review page for September 2008.
 * A script has been used to generate a semi-automated review of the article for issues relating to grammar and house style; it can be found on the automated peer review page for September 2008.

This peer review discussion has been closed. I would like feedback on issues likely to be raised upon nominating this article at FAC so that I can divvy up getting eaten alive between here and there. Copyediting, suggestions on organization and content, and any other comments would be highly valued. Thank you! Emw2012 (talk) 01:48, 9 September 2008 (UTC)

Review of the Lead

I am starting with this section which is the most important. Problems in the Lead often occur again in the body so please cross-check. The article has many good points which I will not dwell on; this is a critical review.
 * The first sentence should mention protein structure solving. This what the project is all about, and this sentence will appear in a Google, or other search.
 * Done.


 * Look out for redundancy like computationally here:
 * Rosetta@home aims to computationally predict protein structures, protein-protein docking and design new proteins with the help of over 86,000 volunteer computers processing over 68 teraFLOPS on average as of September 7, 2008.
 * Done.


 * ...and note that computers do not have free will and cannot volunteer.
 * In this sentence:
 * the project is oriented towards basic research in improving the accuracy and robustness of those proteomics methods - there is a problem with the grammar, it should be research on or research into, and I thin those should be simply the.
 * Done


 * A lot of redundancy here:
 * Rosetta@home also does applied research to address diseases like malaria and Alzheimer's disease. The  to address diseases like simply means on.
 * I was trying to think of ways to mention that Rosetta@home does applied on malaria, Alzheimer's disease and other diseases, but didn't want to use the word 'diseases' twice so closely together. "Pathologies" seems better than "diseases like", but not by much.


 * Later with have volunteer computers again.
 * Changed to "volunteers' computers".


 * This phrase is woolly:
 * to perform calculations on individual workunits, which are sent to a central project server where they are validated and assimilated into project databases upon completion - Presumably it is the results that are sent. This should be said straight away: The results are sent ...
 * Fixed.


 * Never use upon when on will do.
 * Done.


 * Check to see if disease related should be hyphenated.
 * I hyphenated it early on, but changed my mind because the main source used in the 'Disease related research' section (http://boinc.bakerlab.org/rosetta/rah_medical_relevance.php) features the phrase, unhyphenated, in its title. The hyphenation does make it less ambiguous though, so I fixed it.


 * Here, structural bioinformatics has not been aforementioned, well not directly. I would avoid using terms aforementioned or see below, (not that I have seen one yet), readers and reviewers do not like these.
 * Done.


 * Here is some repetition:
 * large and diverse collection of volunteer computers - this could be simply volunteers' computers.
 * The phrase "large and diverse" isn't fluff. Testing software on many different software and hardware is important in alpha and beta products (which RALPH@home and Rosetta@home respectively are, in part).  The phrase indicates the robustness of the testing.  Unless it's a really stylistically jarring, I'd prefer to at least get a second opinion before making your suggested change. Changed "volunteer" to "volunteers'"

More later. Graham Colm Talk 09:41, 10 September 2008 (UTC)

Computing platform
 * This section: Remote and local control of the BOINC client use port 31416 and port 1043, which may need to be specifically unblocked if they are behind a firewall. - Seems to have mixture of singular and plural, and "may" should be "might".
 * In that case I'm referring to 'remote' and 'local' as separate things, which I believe makes it plural. Could you point out the mixture? Made "may" "might".


 * Here we have tautology with regard to structure: Depicted immediately to the right of this is the structure of the most recent accepted structure.
 * This -> that


 * Whenever you write in other words, seriously consider deleting the sentence that precedes it and then deleting "In other words".
 * Done


 * I think this hours of the day means "times".
 * To avoid readings thinking that one of the project's preferences is limiting how many instances of Rosetta@home can run (e.g., only three times, or perhaps three program instances), I've amended that phrase to "times of the day".


 * Presumably, underlying application means "software"?
 * Done.


 * Facilitate = allow?
 * Done.


 * I don't like debuted
 * Changed to "released".


 * Here, The software is freely licensed to the academic community; it is available to pharmaceutical companies through a fee. I suggest you remove the semi-colon and write and.
 * Done

Protein significance


 * This is a poor heading; how about Protein structure, docking and design?
 * The heading is actually 'Project significance', not 'Protein significance'. While the section is fairly oriented towards the significance of protein structure and docking prediction and protein design and how Rosetta features into that, I would not be too opposed if you still think it should be retitled.  Let me know though.


 * Here, With the proliferation of genome sequencing projects, scientists can infer the amino acid sequence, or primary structure, of many proteins that carry out various functions within the cell. In order to better understand a protein's function and aid in rational drug design, scientists need to know the protein's 3-dimensional, tertiary structure. - I would dump various and definitely dump in order to; it's just to.
 * Done


 * I notice you using Emdashs and Endashes, please check with WP:MOS that you have got them correct.
 * After looking at En dash versus em dash, I think I do.


 * Here, in which researchers from around the world attempt to provide a protein's structure from the protein's amino acid sequence - I don't think provide is the best word, perhaps, derive or predict or prove?
 * Agreed, fixed.


 * I would avoid CASP5 with the number, just put CASP and the year.
 * In both journals and the Rosetta@home site, specific CASP experiments are usually specified by number instead of year. If it's enough of a problem I can change it, but I can imagine readers looking at "in the 2002 CASP competition" and counting back from CASP 8 by pairs of years to figure out which CASP that referred to.


 * Generally, I would not recommend using Latin, particularly ab intio so much, and where there is as well as, this should just be and.
 * The phrase  ab initio or de novo is central to what Rosetta@home does. The alternative description,  using a phrase like "prediction made without sequence or structural homology", is awkward and probably more bewildering.  I also can't think of a suitable alternative for the only other Latin phrase I used ("de facto standard-bearers"), but there may be one.  I changed all instances of "as well as" to "and"


 * I would delete hard-gotten, (they probably got lesser mortals to do all the hard work in anycase).
 * I changed it to "particularly difficult-to-obtain", because it indicates that one of RosettaDock's biggest appeals is that it models particularly difficult-to-crystallize protein-protein interfaces, which are uncooperative to begin with.


 * Here we have big problems with snaking sentences which must be chopped up:
 * Development of RosettaDock diverged into two branches for subsequent CAPRI rounds as Jeffrey Gray, who laid the groundwork for RosettaDock while at the University of Washington, continued working on the method in his new position at John Hopkins University, and members of the Baker laboratory further developed RosettaDock in Gray's absence. The two versions differed slightly in side-chain modeling, decoy selection and other areas,[30][50] but both the Baker and Gray methods performed well in the second CAPRI assessment, placing fifth and seventh respectively out of 30 predictor groups.


 * The method used a fast, crude docking model phase using only the protein backbone, followed by a slow full-atom refinement phase in which the orientation of the two interacting proteins relative to each other, as well as side-chain interactions at the protein-protein interface, were simultaneously optimized to find the lowest energy conformation. . The vastly increased computational power afforded by the Rosetta@home network, in combination with revised "fold-tree" representations for backbone flexibility and loop modeling, made RosettaDock sixth out of 63 prediction groups in the third CAPRI assessment.
 * Fixed.

That's all from me. I suggest you get another opinion; I'm not very hot on WP:MOS. And, by the way, it's a very interesting article. Graham Colm Talk 15:54, 10 September 2008 (UTC)
 * Thank you so much! Getting input from an experienced editor is something this article had very much been in need of, before you and Mattisse came along.  I'll go with your advice and get another source of input before nominating it for FA. Emw2012 (talk) 22:39, 11 September 2008 (UTC)