Publication/Paper (NAR 2012)/Corrections

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Corrections to the proof (NAR-GKR1058)

If you've found this page, you should have received the proofs by email. Please do not publicise the proofs, as required by NAR.

I write the following statement because NAR requested, if authors want to make substantial change, then we need to contact the executive editor.

  • The authors consider all the proposed changes necessary. These changes will make the final version more reader friendly and easier to understand. No content is proposed to be changed after the peer-review process. No substantial change is suggested. The authors thus hope all suggested corrections to be incorporated into the final version

Corrections in 4-line FORMAT

Illustration of the 4-line format

  • Page and the line appear in gkr1058.pdf
    • Original sentence appear in gkr1058.pdf
    • Replacement: The sentence authors want to be used to replace the original sentence
Authors’ explanation of the changes
  • Points to note
  1. The sentences are quoted with “”
  2. If the text spans more than 1 line, the lines affected (as in gkr1058.pdf) are marked inside <>, e.g. <line 23>


  • There are 38 corrections, as listed below:

Correction 1

  • PAGE 1, LINE 16-17
    • “However, the increasing throughput of these technologies has created many challenges ...”
    • “However, the increasing throughput of these technologies has also created many challenges ...”
REJECTED: The word 'also' is redundant here because the sentence starts with a 'however' clause, which implies that the same subject is also being discussed.

Correction 2

  • PAGE 1, LINE 21-22
    • "As technologies continue to develop ..."
    • "As technologies continue to be developed ..."
Technologies do not develop themselves.

Correction 3

  • PAGE 1, LINE 42-43
Can you put the URL on line 43 instead of breaking it over line 42-43. This would look much neater. For consistency, please capitalize “SEQ”.

Correction 4

  • PAGE 1, LINE 49
    • “... for novel analysis.”
    • “... for data analysis.”
“data analysis” is a more appropriate term. “novel analysis” is not the meaning the authors want to convey.

Correction 5

  • PAGE 1, LINE 55-56
    • “... are deprived of opportunities for understanding.”
    • “... are deprived of opportunities to understand the tools published there.”
The sentence ending with “understanding” will confuse the reader, it's better to explicitly tell the reader what kind of understanding the authors mean.

Correction 6

  • PAGE 1, LINE 57
    • "The rapid emergence of tools is exceeding ..."
    • "The rapid emergence of tools for HTS analysis is exceeding ..."
We need to be explicit about the type of tools emerging.

Correction 7

  • PAGE 1, LINE 61
    • “Traditionally, practices such as journal clubs have been ...”
    • “Traditionally, practices such as journal club have been ...”
Journal club should be a singular noun here. The authors want to say journal club is one kind of practices that have been used. REJECTED I see what you're getting at, but this is one of those cases where the correct pluralization sounds wrong. The plural form is also not unacceptable, and 'sounds right'. Actually, if we are just talking about one kind of practice, we shouldn't pluralize 'practices', which I think is where the 'sounds wrong' comes from (plural singular agreement). However, because we are referring to possible practices, the plural here is fine. i.e. "Shops such as TK Max have..." (sounds fine, but "X such as journal club have..." sounds wrong).

Correction 8

  • PAGE 1, LINE 64-65
    • “... usually within an institution or local region, and the limited number of topics ...”
    • “... usually within an institution or local region. The limited number of topics ...”
Correct the running sentence which might confuse the reader otherwise.

Correction 9

  • PAGE 1, LINE 67
    • "All these issue a call for a robust ..."
    • "All these issues call for a robust ..."
Typo.

Correction 10

  • PAGE 2, LINE 1
    • “... gaining in popularity (3).”
    • “... gaining popularity (3).”
REJECTED Why?

Correction 11

  • PAGE 2, LINE 6
    • “... cannot fully encompass the ...”
    • “... cannot fully encompasses the ...”
REJECTED I can't work out precisely why this is wrong, it's just wrong. X encompasses Y, true. X cannot encompasses Y, false.

Correction 12

  • PAGE 2, LINE 20
    • “The community allows new ...”
    • “The forum allows new ...”
The authors noticed there is another “community” at the end of the sentence. Also, it is the forum specifically that allows tools, technologies and pipeline to be announced. It is more precise to use the term “forum”.

Correction 13

  • PAGE 2, LINE 26
    • “... user-driven resource, focused on all ...”
    • “... user-driven resource that focus on all ...”
REJECTED The phrase 'that focus on' is wrong in this context, I think because we talk about the forum, singular. Several forums may focus on x, a single forum focuses on x.

Correction 14

  • PAGE 2, LINE 35
    • “... ideas and review of findings between peers ...”
    • “... ideas, findings and reviews between peers ...”
Ideas and findings are two separate things.

Correction 15

  • PAGE 2, LINE 35-36
    • “... at the cutting edge of high-throughput genome biology.”
    • “... at the cutting edge of high-throughput genomics.”
This is a more appropriate term here.

Correction 16

  • PAGE 2, LINE 38-40
    • “SEQanswers allows interaction among bioinformatics analysts and dynamic interaction between users and developers.”
    • “SEQanswers allows interaction among bioinformatics analysts and between users and developers.”
Repetition of 'dynamic interaction' was redundant.

Correction 17

  • PAGE 2, LINE 41-43
    • “Traditional software release in the form of email announcements or on a tool’s website require the users’ prior interest in the tool.”
    • Traditional software release, in the form of email announcements or on a tool’s website, require the users prior interest in the tool.
Trying to clarify the sentence to make it easier to understand.

Correction 18

  • PAGE 2, LINE 46-47
    • “Developer feedback via traditional channels is usually private”
    • “Feedback to developers via traditional channels is usually kept private”
    • REJECTED I think it's clear enough. The meaning is identical.

Correction 19

  • PAGE 2, LINE 48-49
    • "Ideas are rapidly developed, and theoretial issues are debated."
    • "Ideas are rapidly developed, practical and theoretical issues are debated."
We missed the word "practical" in the revised version.

Correction 20

  • PAGE 2, LINE 55
    • “... where an ever growing list of software was being collected.”
    • “... where an ever growing list of software was being maintained.”
The verb followed “being” refer to the “growing list”, so the list should be maintained.

Correction 21

  • PAGE 2, LINE 56-57
    • “... it lacked collaborative editing and categorization of resources.”
    • “... collaborative editing and categorization of resources was inefficient”
The replacement sentence better describe the SEQanswers forum. REJECTED I don't think so, there was no way to collaboratively edit the forum post.

Correction 22

  • PAGE 2, LINE 66
    • “... (i) software, (ii) service providers and (iii) tutorials.”
    • “... (i) software, (ii) service provider and (iii) tutorial.”
Noun for the category should be singular. REJECTED This grammatical advice may be true, but it just sounds wrong here. Not sure why.

Correction 23

  • PAGE 2, LINE 78-79
    • "... formats using either forms or regular ‘wiki text’, respectively."
    • "... format using either forms or regular ‘wiki text’, respectively."
REJECTED format or formats is equally fine here. To reduce the number of corrections, I'm rejecting minor issues like this.

Correction 22

  • PAGE 2, LINE 92-93
    • “and the types of compatible HTS technology.”
    • “and the type(s) of compatible HTS technologies.”
    • typological error

Correction 23

  • PAGE 3, LINE 1
    • “and a tool is discoverable”
    • “and a tool can be discovered”
    • grammatical mistake

Correction 24

PAGE 3, LINE 9-10
change "user to search for the tool in a variety of resources" to "user to perform search of the tool against a variety of resources"
  • PAGE 3, LINE 9-10
    • “user to search for the tool in a variety of resources,”
    • “user to perform search of the tool against a variety of resources,”
    • typological mistake.

Correction 25

  • PAGE 3, LINE 30
    • “providers from around the globe”
    • “providers around the globe”
    • delete “from” before “around”. Typological mistake

Correction 26

  • PAGE 3, LINE 51
    • “along with advantages,”
    • “along with their advantages,”
    • Add “their” before advantages, so to make the sentence easier to understand.

Correction 27

PAGE 3, LINE 58-59
delete the "that" between "activity, but" and "there has been a" , so it reads "bursts of activity, but there has been a trend"
  • PAGE 3, LINE 58-59
    • “but that there has been a”
    • “but there has been a”
    • delete “that” before “there”, so that the complete sentence is “but there has been a trend of ….”

Correction 28

  • PAGE 4, LINE 7
    • “features of the wiki, in parcitular, we”
    • “features of the wiki. In particular, we”
    • Typological mistake. The authors corrected the running sentence

Correction 29

  • PAGE 4, LINE 9-10
    • “Community review system: before SEQanswers, user”
    • <in line 9> “Community review system:”
   <in line 10> “Before SEQanswers, user”
    • Move the sentences one line under the the topic “Community review system”

Correction 30

  • PAGE 4, LINE 28-29
    • “Community-wide benchmarking: Systematic benchmarking”
    • <line 28> “Community-wide benchmarking:”
 <line 29> “Systematic benchmarking”
    • Move the sentences one line under the the topic “Community-wide benchmarking”

Correction 31

  • PAGE 4, LINE 35
    • “By using the wiki, we would aim to”
    • “By using the wiki, we aim to”
    • delete “would” before “aim”

Correction 32

  • PAGE 4, LINE 40-41
    • “be motivated to provide information on their tools”
    • “be motivated to provide information of their tools”
    • change “on” to “of”

Correction 33

  • PAGE 4, LINE 41-42
    • “users would be motivated to feedback the results”
    • “users would be motivated to return the results”
    • replace “feedback” by “return”

Correction 34

  • PAGE 4, LINE 44-45
    • “Integration with the semantic web: there are several”
    • <line 44> “Integration with the semantic web:”
   <line 45> “There are several”
    • Move the sentences one line under the the topic “Integration with the semantic web”

Correction 35

  • PAGE 4, LINE 46
    • “sciences using ontologies, for example, the”
    • “sciences using ontologies. For example, the”
    • Typological mistake. The authors corrected the running sentence

Correction 36

Correction 37

  • PAGE 5, LINE 31-32
    • <line 31> “The discussion where SEQwiki originated: http://”
    <line 32> “seqanswers.com/forums/showthread.php?t=43”
    • <line 31> “The discussion where SEQwiki originated:”
    <line 32> “http://SEQanswers.com/forums/showthread.php?t=43”
    • Move http:// at line 31 to line 32 so that the link is placed entirely on line 32. ALSO, change "seqanswers.com" to "SEQanswers.com", i.e. capitalize SEQ in the domain name

Correction 38

  • PAGE 5, LINE 43-44
    • <line 43> “Critical Assessment of Genome Interpretation: http://”
    <line 44> “genomeinterpretation.org/”
    • <line 43> “Critical Assessment of Genome Interpretation:”
     <line 44> “http://genomeinterpretation.org/”
    • Move http:// at line 43 to 44 so that the link of Critical Assessment of Genome Interpretation is entirely on line 44

Correction 39

  • PAGE 5, LINE 45-46
    • <line 45> “Genome Assembly Gold-Standard Evaluations:”
    <line 46> “gage.cbcb.umd.edu/”
    • <line 45> “Genome Assembly Gold-Standard Evaluations:”
    <line 46> “http://gage.cbcb.umd.edu/”
    • Move http:// at line 45 to 46 so that the link for Genome Assembly Gold-Standard Evaluations is entirely on line 46

Replies to QUESTIONS 1-10

Q1

(1a) Annotation

A '*' appears after Dan M. Bolser, but should also appear after Jing-Woei Li and Eric C. Olivares too.

(1b) Name

Name - please refer back to gkr1058.pdf sent out by Dan


  • Jing-Woei Li : Name is alright for me.
  • Keith Robison: Name is alright (replied by email)
  • Marcel Martin: Name is alright (replied by email)
  • Andreas Sjo¨din: Name is alright (replied by email). Note: make sure the two dots are above "o", yes, they appear to be correctly displayed in the proof pdf
  • Bjo¨ rn Usadel: Name and affiliation correct in proof and here
  • Matthew Young: Name is alright (replied by email)
  • Eric C. Olivares: Name is alright (no correction made in email)
  • Dan M. Bolser: (Author names look fine to me)

Q2

Institution - please check if you institution's name is correct. Add your department (if any)

  • Jing-Woei Li : Institution looks ok to me
  • Keith Robison: Warp Drive Biosynthetics, 215 First St., 4th Floor, Cambridge MA 02142 [Institution is alright (replied by email)]
  • Marcel Martin: Institution is alright (replied by email)
  • Andreas Sjo¨din: Institution is alright (replied by email). Make sure a circule appear above "a" in "Umea". Yes, it appears to be OK in the proof pdf
  • Bjo¨ rn Usadel: correct (see above Q1)
  • Matthew Young: Institution is alright (replied by email)
  • Eric C. Olivares: Institution is alright (no correction by email)
  • Dan M. Bolser:

Q3

  • Dan M. Bolser's email address is typed incorrectly in the proof copy. It should be "dan.bolser@gmail.com", Dan M. Bolser doesn't have a fax number. Please advise
  • Jing-Woei Li, Wants to use "marcowanger@gmail.com" instead of "marcoli@cuhk.edu.hk", Tel. +852 3943 1256 ;Fax. Do not have a fax number. Please advise
  • Eric Olivares, Tel. 011 1 760 419 5118 Fax. Do not have a fax number. Please advise

Q4-7

References accuracy:

  • 1st pass (Marco): See below
  • Q4 (all ref): All references information already in the proof version is accurate. Please incorporate the detailed information we answered in Q5-7 into the references.
  • Q5 (publisher name and location in ref 2): The Royal Society; 6 - 9 Carlton House Terrace, London SW1Y 5AG
  • Q6 (complete name of Proceedings in ref 7): alt.CHI at 25th Annual ACM Conference on Human Factors in Computing Systems (CHI 2007)
  • Q7 (DOI number and E-publicaiton date in Ref 8): DOI: 10.1101/gr.126599.111 E-publication date: Sep 16 2011
  • 2nd pass (Dan & Marco):
  • Marco: To be done
  • Dan: To be done

Q8

We haven't received any funding for this SEQwiki project.

Q9

Done. Figures and figure legends look great!

Q10

All figures must be in color.

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