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.

Corrections in 4-line format

Please refer to the google doc here

Correction.1

• I suggest to send the .doc file & pdf to OUP instead of pasting them to email (because of the highlight and formatting)
• After going through the Correction.1, I will make the changes on .doc and pdf.

Corrections in LIST FORMAT - FREEZED. Please refer to the above 4-line format

Please do not delete the content below. --Marcowanger 05:27, 6 November 2011 (PST)

• Be careful during proof-reading, there are multiple subtle changes to our revised MS shown in this proof-copy.
• I will visualize the changes in word document. Just to make sure the editor know what change is needed.
• 4-line correction: <page & line>\n<original>\n<changed>\n<remarks>
• Dan, please go over the list after I finished the correction part.

PAGE 1, bottom

Check Dan's email address for correspondence dan.bosler@gmail.com

PAEG 1, LINE 17

add "also" before "created", so it reads "technologies has also created many"

PAGE 1, LINE 21-22

As technologies continue to develop. Should change to "continue to be developed". technologies do not develop themselves.

PAGE 1, LINE 42-43

The URL should be "http://wiki.SEQanswers.com/" <- suggested by Marco: Keep the domain name consistent, should we use xxx.SEQanswers.com or xxx.seqanswers.com?

PAGE 1, LINE 42-43 

We suggest the URL be placed on line 43 instead of being broken over line 42-43. This would look much neater.

PAGE 1, LINE 49

replace "novel" by "data", so it reads "for data analysis. Both biologists"

PAGE 1, LINE 52

change "choice" to "choices", so it reads "more choices does not necessarily"

PAGE 1, LINE 55-55

Change "deprived of opportunities for understanding." to "deprived of opportunities to understand the tools published there."

PAGE 1, LINE 61

Change "journal clubs" to "journal club" <- Marco, journal club is a noun. practices are many, journal-club is one of them. so plural does not applies here.

PAGE 1, LINE 65

Change "region, and the limited" to "region. And the limited"

PAGE 2, LINE 1

delete "in" before "popularity", so it reads "gaining popularity"

PAGE 2, LINE 6

change "encompass" TO "encompasses"

PAGE 2, LINE 20

Change "community" to "forum", so it reads "The forum allows new"

PAGE 2, LINE 26

change "is a broad, user-driven resource, focused.." to "is a broad, user-driven resource that focus on all"

PAGE 2, LINE 35

change "ideas and review of findings between peers" to "ideas and findings among peers"

PAGE 2, LINE 36

Change "genome biology" to "genomic science"

PAGE 2, LINE 41-42

The sentence should be "Traditionally, announcement about software in the form of email or notice on tool's website".

PAGE 2, LINE 46-47

Change "Developer feedback via traditional channels is usually private" to "Feedback to developer via traditional channels is usually kept private"

PAGE 2, LINE 55

change "of software was being collected" to "of software was being maintained"

PAGE 2, LINE 56-57

change "it lacked collaborative editing and categorization of resources" to "collaborative editing and categorization of resources was inefficient."

PAGE 2, LINE 66

All categories should be singular here. "service provider" and "tutorial".

PAGE 2, LINE 77-78

change "free text formats" to "free text format"

PAGE 2, LINE 92-93

change "and the types of compatible HTS techonology" to "and the type(s) of compatible HTS technologies"

PAGE 3, LINE 1

change "tool is discoverable" to "can be discovered"

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 30

change "providers from around the globe" to "providers around the globe". i.e. delete "from"

PAGE 3, LINE 51

change "along with advantages" to "along with their advantages"

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 4, Not specific to lines. To all areas that we would like to improve. The (i), (ii) and (iii) wasted a lot of space (already narrow as 2 column in A4). I suggest remove these symbols and let them appear as separate paragraphs.

PAGE 4, LINE 7

Change "of the wiki, in particular" to " of the wiki. In particular"

PAGE 4, LINE 9 

The first word after colon should start be capitalized. i.e. after Community review system: "before" should be changed to "Before".

PAGE 4, LINE 35

delete "would", so it reads "By using the wiki, we aim to distribute and"

PAGE 4, LINE 40-41

change "on" to "of", so it reads "provide information of their tools,"

PAGE 4, LINE 42

change "feedback the results" to "return results"

PAGE 4, LINE 44 

The first word after colon should start be capitalized. i.e. after Integration with the semantic web: "there" should be changed to "There".

PAGE 4

LINE 46: Change "ontologies, for example" to "ontologies. For example"<- Marco: running sentence

PAGE 5; After LINE 30

Add "Papers Referencing SEQanswers: http://SEQanswers.com/wiki/Papers_Referencing_SEQanswers". Again, the we request the link to be entirely placed on one line if possible.

PAGE 5, LINE 31-32

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

PAGE 5, LINE 43-44

Move http:// at line 43 to 44 so that the link of Critical Assessment of Genome Interpretation is entirely on line 44

PAGE 5, LINE 46

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. We have requested for full waiver.

Q9

Done. Figures and figure legends look great!

Q10

All figures must be in color.