Publication/Paper (NAR 2012)/Corrections

Corrections to the proof (NAR-GKR1058)

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• The authors consider all the proposed changes necessary. These changes will make the production-copy more reader friendly and easier to understand. No content is proposed to be changed after the peer-review process.

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

The sentences are quoted with “” If the replacement span more than 1 line, the lines affected (as in gkr1058.pdf) is marked inside <>, e.g. <line 23>

• There are 38 corrections, as listed below,

Correction 1

• PAEG 1, LINE 17
  • “these technologies has created many challenges”
  • “these technologies has also created many challenges”
  • Add “also” between “technologies” and “created many challenges”

Correction 2

• PAGE 1, LINE 21-22
  • As technologies continue to develop
  • As technologies continue to be developed
  • technologies do not develop themselves, they are being developed

Correction 3

• PAGE 1, LINE 42-43
  • <line 42> http://wiki

    <line 43>.seqanswers.com/

• • <line 43> http://wiki.SEQanswers.com/.
  • Please put the URL of SEQanswers wiki into one single line. AND 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 52
  • “more choice does not necessarily”
  • “more choices does not necessarily”
  • “choice” should be plural here, so “choices”

Correction 6

• PAGE 1, LINE 55-56
  • “deprived of opportunities for understanding.”
  • “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 7

• PAGE 1, LINE 61
  • “practices such as journal clubs”
  • “practices such as journal club”
  • journal club should be a singular noun here. The authors want to say journal club is one kind of practices that have been used.

Correction 8

• PAGE 1, LINE 65
  • “local region, and the limited”
  • “local region. And the limited”
  • Correct the running sentence which might confuse the reader otherwise.

Correction 9

• PAGE 2, LINE 1
  • “gaining in popularity”
  • “gaining popularity”
  • delete the “in” before “popularity”

Correction 10

• PAGE 2, LINE 6
  • “cannot fully encompass the”
  • “cannot fully encompasses the”
  • encompass refer to (a small group), so authors think “encompasses” should be used rather than “encompass”

Correction 11

• 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 12

• PAGE 2, LINE 26
  • “user-driven resource, focused on all”
  • “user-driven resource that focus on all”
  • typological error

Correction 13

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

Correction 14

• PAGE 2, LINE 36
  • “of high-throughput genome biology”
  • “of high-throughput genomic science”
  • Authors want to use a more appropriate term “genomic science” in this line.

Correction 15

• 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.”
  • “Traditionally, announcement about software in the form of email or notice on tool’s website require the users’ prior interest in the tool.”
  • Authors want to clarify the sentence to make it easier to understand.

Correction 16

• PAGE 2, LINE 46-47
  • “Developer feedback via traditional channels is usually private”
  • “Feedback to developer via traditional channels is usually kept private”
  • Authors want to clarify the sentence to make it easier to understand.

Correction 17

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

Correction 18

• 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.

Correction 19

• 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.

Correction 20

• PAGE 2, LINE 77-78
  • formats using either forms or regular ‘wiki text’,”
  • format using either forms or regular ‘wiki text’,”
  • The first letter of the sentence “format” should be singular

Correction 21

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

Correction 22

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

Correction 23

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 24

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

Correction 25

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

Correction 26

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 27

• 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 28

• 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 29

• 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 30

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

Correction 31

• 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 32

• 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 33

• 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 34

• 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 35

• PAGE 5, After LINE 30
  • <There is no original sentence>
  • “Papers Referencing SEQanswers: http://SEQanswers.com/wiki/Papers_Referencing_SEQanswers"
  • We request that, if possible, the link to be placed entirely on one single line.

Correction 36

• 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 37

• 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 38

• 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 :
• 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:
• 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 doesn't have a fax number. Please advise
• Jing-Woei Li, 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): To be done
• 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.