Folding Forum

The English-language pages need copyediting. Badly. Just a few examples: Something in one of the FAQs has lead to a major jump. Did you know that calculations have become routine? Are you helping fight from having duplicate IDs? I would dearly love to to the job, but I can't find a way to e-mail any webmaster-like person about it. Who[m] do I call?

Rasmunsen wrote:The English-language pages need copyediting. Badly. Just a few examples: Something in one of the FAQs has lead to a major jump. Did you know that calculations have become routine? Are you helping fight from having duplicate IDs? I would dearly love to to the job, but I can't find a way to e-mail any webmaster-like person about it. Who[m] do I call?

Hello Rasmunsen, welcome to the folding forum.

If you could provide a more specific example of the needed edits, such as the exact page URL, and the text that should be updated, we can make sure that gets updated or corrected. Just post the info here in the forum.

Also, the "About Us" link on the project home page will lead you to the project group page (Pande Group), the leader of that group (Vijay Pande), and eventually to a page with his email address.

Hi, O great wizard or whatever. Thanks for the reply. I can address the problems with the text the way you say, but there are a million errors, and it will take forever that way. Also, as much as you are having trouble believing that I know what I'm doing and can be trusted to do it, I am having trouble believing that the corrections I suggest here will be made, because if anybody on your side could tell the difference the errors would have been corrected before now, so how will you know whether I'm right or not? And committees are notoriously bad at copyediting. But, OK, to make a start:

http://folding.stanford.edu/:
*What is protein folding and how is folding linked to disease? [Needs a comma linking the two independent clauses: What is protein folding, and how is folding linked to disease?]

*Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes. ["I.e." takes a comma, it's "well-known", and, if I had my druthers, "cancers".]

*Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved. [Lose the unnecessary comma: Folding@home uses novel computational methods coupled to distributed computing to simulate problems millions of times more challenging than previously achieved.]

*You can read about them on our Science page, on our Awards page, or go directly to our Results page. [Faulty parallelism; the items in a list must be of the same kind, and here we have two prepositional phrases and an imperative clause. Maybe: You can read about them on our Science page and on our Awards page, or go directly to our Results page.]

Ahem. Self-fulfilling prophecy? Or what?

PM sent.

OK, forging ahead:

http://folding.stanford.edu/English/FAQ-Diseases

*We feel strongly that a Distributed Computing project must not just run calculations on millions of PC's, but DC projects must produce results, especially in the form of peer reviewed publications, public lectures, and other ways to disseminate the results from FAH to the greater scientific community. Below, we also detail our progress in these areas as well. [There is no justification for the caps in "Distributed Computing", and if we will later refer to it as "DC", we have to clue the reader in here: "We feel strongly that a distributed computing (DC) project must not just run calculations ...". It's "PCs", no apostrophe, and "peer-reviewed" with a hyphen. "Other ways to disseminate" doesn't ring idiomatic; try "of disseminating". "As well" makes "also" redundant: "Below, we detail our progress in these areas as well."]

*What is protein folding and how is it related to disease? [Normally, a comma is required between two independent clauses: What is protein folding, and how is it related to disease? Some might say that this falls under the exception that short, parallel clauses can do without it, but I don't, it can't hurt, and it relieves the reader of the task of deciding on the fly where we're going with "how".]

*In order to carry out their function (e.g. as enzymes or antibodies), they must take on a particular shape, also known as a "fold." ["E.g." takes a comma: In order to carry out their function (e.g., as enzymes or antibodies), they must take on a particular shape, also known as a "fold." This is invariable.]

*AD is caused by the aggregation of relatively small (42 amino acid) proteins, called Abeta peptides. [I can't say I like hyphens. They are a necessary evil at best, a bugaboo at slightly worse, and a blight at worst. Here, they are the first thing: AD is caused by the aggregation of relatively small (42-amino-acid) proteins, called Abeta peptides.]

*September 2006: We have submitted our first paper for peer review and we're working on the next 2 paper right now. [I guess he meant "next two papers", and linking comma: We have submitted our first paper for peer review, and we're working on the next two papers right now.]

*If these cells didn't die, their damaged DNA would lead to the strange and unusual growths found in cancer tumors and this growth would continue unchecked, until death. [Linking comma, lose the extra one: "If these cells didn't die, their damaged DNA would lead to the strange and unusual growths found in cancer tumors, and this growth would continue unchecked until death.]

*In collaboration with other groups at Stanford (especially Dr. Teri Klein's group at Stanford University Medical Center), we are looking at Collagen folding and misfolding. Collagen is the most common protein in the body and mutations in collagen leads to a very nasty disease called Osteogenesis Imperfecta (or OI for short). In many cases, OI is lethal and leads to miscarriage. However, 1 in 10,000 people have some sort of mutational in collagen. [Lowercase "collagen". Linking comma, and although I appreciate the dilemma that led to the <strike>double</strike> singular plural, it's better to let "mutation" take the general construction: Collagen is the most common protein in the body, and mutation in collagen leads to a very nasty disease called Osteogenesis Imperfecta (or OI for short). I'm looking at: In many cases, OI is lethal to the unborn child and leads to miscarriage. I'm not sure whether "mutational" is jargon or a mistake, but either way, I'd like to see "mutation" instead: However, 1 in 10,000 people have some sort of mutation in collagen.]

*The Ribosome is an amazing molecular machine and plays a critical role in biology, as it is the machine that synthesizes proteins. Because of this critical role, and some small but fundamental differences in the ribosomes of mammals and bacteria, the ribosome is the target for about half of all known antibiotics. These antibiotics typically work by preventing bacterial ribosomes from making new proteins, thus killing them. We have several projects on going to study the ribosome. Since the ribosome is so huge, these WUs are big WUs and have required us to push the state of the art of FAH calculations. However, with these new bigWUs, FAH is set up to study more and more complex problems, and if successful, with greater and greater biomedical impact. [Lowercase "ribosome" and faulty parallelism: The ribosome is an amazing molecular machine that plays a critical role in biology, as it is the machine that synthesizes proteins. Killing whom?: These antibiotics typically work by preventing bacterial ribosomes from making new proteins, thus killing the bacterium. (Sorry about that one, but I thought, "While I'm here...".) A parenthetical needs to be bracketed by commas: However, with these new bigWUs, FAH is set up to study more and more complex problems, and, if successful, with greater and greater biomedical impact.]

*April 2007: We have received a grant from Stanford University to design and study novel antibiotics. This grant is joint with the labs of Chaitan Khosla at Stanford's Chemistry Department (who does small molecule synthesis, design, and some characterization) and Jody Puglisi at the Stanford Medical School (who studies the ribosome and antibiotics experimentally) [Needs a period (full stop) at the end.]

*While it gives computer resources much greater than a typical supercomputer (e.g. the almost 200,000 actively processing CPUs in FAH vs. 5,000 in a typical supercomputer), these processors are connected by the Internet, not the high speed, low latency interconnects found in supercomputers. ["Gives" is staggering, "e.g." comma, and those bloody hyphens: While it affords computer resources much greater than a typical supercomputer (e.g., the almost 200,000 actively processing CPUs in FAH vs. 5,000 in a typical supercomputer), these processors are connected by the Internet, not the high-speed, low-latency interconnects found in supercomputers.]

*We will continue to work on all fronts: new scientific cores, new server side algorithms.... [Hyphen: ...server-side....]

This is as laborious to do as it is to read, believe me, and it seems to make heavy going of simple matters, but in this setting explanations are required. You know what, though? I'll be the first person to have read every word on this site if I finish.

What the hey:

http://folding.stanford.edu/English/Science

*In order to carry out their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." [It's: (e.g., as enzymes ....]

*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. [A colon is too much: ... but they do so amazingly quickly, some as fast as a millionth of a second.]

*Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! [Enough with the I.e.s, already: Thus, it would take 10,000 CPU days to simulate folding -- 30 CPU years!]

*... with a near linear speed up in the number of processors. [Hyphen, and "speedup" is one word as a noun: ... with a near-linear speedup in the number of processors. Also, I can't tell what that means--how can a number speed up?]

*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. [Parenthetical comma: 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? [Comma: What have we done so far, and where are we going?]

*In 2000-2001, we have folded several small, fast folding proteins, with experimental validation of our method. [Wrong tense, hyphen: In 2000-2001, we folded several small, fast-folding proteins, with experimental validation of our method.

*Since then (2002-2006), 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. [Missing "and": Since then (2002-2006), Folding@Home has studied more complex proteins, reporting on the folding of many proteins on the microsecond timescale, including BBA5, the villin headpiece, and Trp Cage, among others.]

*More recently (2006-present), we have been putting a great deal of effort into studying proteins relevant for diseases, such as Alzheimer's and Hunntington's Disease. [Typo: Huntington's]

*How can I learn more about how Folding@home works and what Folding@home has done so far? [Comma: How can I learn more about how Folding@home works, and what Folding@home has done so far?]

*Also, please check out our FAQ and in particular, our page on the diseases and biomedical questions we are studying. [Unneeded, confusing comma: Also, please check out our FAQ and in particular our page on the diseases and biomedical questions we are studying.]

Rasmunsen wrote:... You know what, though? I'll be the first person to have read every word on this site if I finish.

You betcha!

Great stuff though. I'm sure the site administrators appreciate your efforts, and you have the end-user's props too.

P.S. Reading through your corrections has made me look at the commas in this post atleast thrice . One of those times where the more you look, the weirder it appears to be.

I'm baaa-aaack:

http://folding.stanford.edu/English/Awards

*The project uses the power of peoples' home com[puters, as well as their PlayStation3s, to simulate the processes inside living cells that cal lead to diseases, such as Alzheimer's Disease. [I don't have access to the Guinness text, but there are a couple of typos there that I suspect were not in the original. I won't insult anyone's intelligence by naming them.]

*Folding@Home researchers Vishal Vaidyanathan and Nick Kelley win the best talk award at BCATS 2005 for Alzheimer's Disease work. [Lowercase "home", quotes and caps: Folding@home researchers Vishal Vaidyanathan and Nick Kelley win the "Best Talk" award at BCATS 2005 for Alzheimer's Disease work.]

*BCATS is Stanford's symposium on Biomedical simulation. [biomedical]

*These results will soon be submitted for peer reviewed publication. [peer-reviewed]

*This is the third best talk award at BCATS for Folding@Home. [Again: This is the third "Best Talk" award at BCATS for Folding@home.]

*This is the second Protein Society award for Snow and the third for FAH in general, which has won the award in three of the last 4 meetings. [The rule is single-digit numbers get spelled out unless there's a reason not to, and all others get numerals unless there's a reason to spell them out, but consistency trumps everything: This is the second Protein Society award for Snow and the third for FAH in general, which has won the award in three of the last four meetings.]

*November 2004: Folding@Home Founder and Director Prof. Vijay Pande awarded by Global Indus Technovators. The Global Indus Technovators are a group based at MIT has awarded Prof. Pande a Technovator award in the Biotech/Med/Healthcare sector. Technovators2004The Global Indus Technovator Awards have been instituted to recognize and felicitate 20 distinguished innovators of Indus origin working at the cutting-edge of technology that may be harnessed for far-reaching applications. [This is garbled. My best guess at what was meant: November 2004: Folding@home Founder and Director Prof. Vijay Pande named a "Technovator" for 2004 by Global Indus Technovators. The Global Indus Technovators, a group based at MIT, has awarded Prof. Pande a "Technovator" award in the Biotech/Med/Healthcare sector. The Global Indus Technovator Awards were instituted in 2003 to yearly recognize and felicitate 20 distinguished innovators of Indus origin working at the cutting edge of technologies that may be harnessed for far-reaching applications. ("Felicitate", indeed. Indian English is simply adorable sometimes.)]

*October 2004: Folding@Home team member Guha Jayachandran wins top award at BCATS 2004. [home]

*Guha gave an invited talk on his work on protein folding and the advances possible with the power of Folding@Home. [home]

*In the four years that BCATS has been run, this is the fourth time a Folding@Home team member has given an invited talk and the second time that the Folding@Home team has won the top prize. [home (twice)]

*The Nature paper by Chris Snow et al from Folding@Home was considered to be one of the "hot papers" from 2003. Check out the ISI web site http://www.esi-topics.com/nhp/2004/janu ... Pande.html for more details. [The Nature paper by Chris Snow, et al., from Folding@home was considered to be one of the "hot papers" from 2003. Check out the ISI web site http://www.esi-topics.com/nhp/2004/janu ... Pande.html for more details.]

*October 2002: Folding@Home team member Bojan Zagrovic wins top award at BCATS 2002. [home]

*BCATS is Stanford's symposium on Biomedical simulation. [biomedical]

*Both Bojan Zagrovic and Chris Snow from the F@H team were invited to give talks and Bojan received the top prize. [Comma and consistency: Both Bojan Zagrovic and Chris Snow from the FAH team were invited to give talks, and Bojan received the top prize.]

*September 2002: Lead Folding@Home developer Guha Jayachandran named as a Siebel Scholar. [September 2002: Lead Folding@home developer Guha Jayachandran named Siebel Scholar.]

*The award was presented to Stefan Larson, lead researcher for the Genome@home project, for his poster, entitled, "Searching sequence space by large-scale protein design" (Stefan M. Larson, Jeremy L. England, Amit Garg, John R. Desjarlais, and Vijay S. Pande). [Trimmed down and tidied. What the names in parentheses were doing there, I can't imagine: The award was presented to Stefan Larson, lead researcher for the Genome@home project, for his poster "Searching sequence space by large-scale protein design". ]

Whew! I hope I didn't screw that up. All the links are live, by the way.

Thanks for taking the time to make this list of suggestions. We have in the past incorporated many suggested edits from donors. However, in this case, many of your edits are stylistic and actually go against our stylistic preferences (for example, "42-amino-acid" looks strange and is actually against typical scientific convention; there are more examples like this). Most of the edits are commas, capitalization, hyphens, etc which are firmly in stylistic territory. However, I think there are some useful non-stylistic suggestions here too.

Since it's easy to screw up edits of this scale, it only makes sense to do the ones which fit our style and that fix true grammatic errors; ideally, we could start with the most important fixes first. Considering all the suggestions here, it will take one of our team members some time to go through these suggestions and incorporate the ones we like. Thanks for the suggestions, but I suggest listing only the ones which are serious grammatical or spelling errors to start so that we fix the most important ones first and then we can debate stylistic edits afterwards.

If you plan to make future suggestions, could you concentrate on the ones that are most critical? Your first post of the thread point to more critical issues. Let's tackle them first and then deal with the stylistic issues second.