Publication/Paper (NAR 2012)/Corrections

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 23 corrections, as listed below:

Correction 1

• PAGE 1, LINE 21-22
  • "As technologies continue to develop ..."
  • "As technologies continue to be developed ..."

Technologies do not develop themselves.

Correction 2

• 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 3

• PAGE 1, LINE 49
  • “... for novel analysis.”
  • “... for data analysis.”

“data analysis” is a more appropriate term. “novel analysis” is not the meaning we wanted to convey.

Correction 4

• 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 5

• 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 6

• 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 7

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

Typo.

Correction 8

• PAGE 2, LINE 20
  • “The community allows new ...”
  • “The forum allows new ...”

It is the forum specifically that allows tools, technologies and pipeline to be announced. It is more precise to use the term “forum”.

Correction 9

• 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 10

• 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 11

• 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 12

• PAGE 2, LINE 46-47
  • “Developer feedback via traditional channels is usually private”
  • “Feedback to developers via traditional channels is usually kept private”

"Feedback to developers" is the precise meaning we want to convey

Correction 13

• 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 14

• 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 15

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

Typo.

Correction 16

• PAGE 3, LINE 1
  • “... down using multiple parameters, and a tool is discoverable ...”
  • “... down using multiple parameters. A tool can be discovered ...”

Grammatical mistake.

Correction 17

• PAGE 3, LINE 24-25
  • "The score increases for evrty field that is filled in the description of the tool."
  • "The score increases for every field that is filled in for the description of the tool."

Typo.

Correction 18

• PAGE 3, LINE 51
  • “... along with advantages, ...”
  • “... along with their advantages, ...”

Add “their” before advantages, so to make the sentence easier to understand.

Correction 19

• PAGE 4, LINE 6-7
  • “We plan to further enhance the features of the wiki, in particular, we ...”
  • “We plan to further enhance the features of the wiki. In particular, we ...”

Typo.

Correction 20

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

Redundant word usage.

Correction 21

• PAGE 4, LINE 41-42
  • “be motivated to feedback the results of their important individual, and hitherto ...”
  • “be motivated to return the results of their important individual and hitherto ...”

(1) feedback is not a verb, "return" should be used, (2) Grammatical mistake.

Correction 22

• PAGE 5, After LINE 30, ELECTRONIC ADDRESSES

Could all URLs be placed entirely on one line (where possible). For example, the link to BioWikis on line 41-42 looks much neater than the others because it isn't broken across two lines.

Correction 23

• PAGE 5, Line 55
  • "Funding for open access charge: SEQanswers community.
  • "SEQanswers Community. Funding for open access charge: Waived by Oxford University Press.

Please replace as advised.

Replies to QUESTIONS 1-10

Q1

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

Q2

There is no department for affiliation 1.

The full address for affiliation 2 should be: Warp Drive Biosynthetics, 215 First St., 4th Floor, Cambridge MA 02142

The department for affiliation 6 should be: Institute for Biology I

The department for affiliation 9 should be: Department of Bioinformatics

Q3

Dan M. Bolser: The email address should be dan.bolser@gmail.com, not dan.bosler@gmail.com. Tel. should be +44 1223 968 518. No fax number available.

Jing-Woei Li: The email address should be marcowanger@gmail.com, not marcoli@cuhk.edu.hk. Tel. +852 3943 1256. No fax number available.

Eric Olivares, Tel. 011 1 760 419 5118. No fax number available.

Q4

All reference information (except the below) is correct.

Q5-7

Q5 Publisher name and location for ref 2: The Royal Society; 6 - 9 Carlton House Terrace, London SW1Y 5AG

Q6 Complete name of Proceedings for ref 7: alt.CHI at 25th Annual ACM Conference on Human Factors in Computing Systems (CHI 2007)

Q7 DOI number and E-publicaiton date for ref 8: DOI: 10.1101/gr.126599.111 E-publication date: Sep 16 2011

Q8

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

After taking into consideration the above corrections, the funding section will now read: "SEQanswers Community. Funding for open access charge: Waived by Oxford University Press."

Q9

Done. Figures and figure legends look great!

Q10

All figures must be in color.