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 LIST FORMAT

• Be careful during proof-reading, there are multiple subtle changes to our revised MS shown in this proof-copy.
• Everything after <- is not included in the reply. This is just to trace back who suggest the change

• page 1

PAGE 1, LINE 20

I suggest change the plural form of "algorithms" to singular form "algorithms". <-suggested by Marco

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 21-22

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

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. <-suggested by Dan

PAGE 1, LINE 55-55

Append to the ending of the sentence "deprived of opportunities for understanding of tools published there." <- Marco : Have to explicitly tell the reader

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 2

PAGE 2, LINE 26

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

PAGE 2, LINE 41-42

The sentence should be "Traditional software release announcement via email or notice on tool's website". Not software release in the form of email announcement or on atoll's website. <- Marco

PAGE 2, LINE 55

change "of software was being collected" to "of softwares was being maintained" <-Marco. An ever growing LIST of softwareS (plural of software) was being maintained. It is the list being maintained, is it in correct to say the LIST was being COLLECTED.

PAGE 2, LINE 56-57

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

PAGE 2, LINE 66

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

• page 3

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" <- arco

• page 4

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. <-Marco

PAGE 4, LINE 7

Change "of the wiki, in particular" to " of the wiki. In particular" <- Marco

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". <- Marco

PAGE 4, LINE 35

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

PAGE 4, LINE 40-41

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

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". <- by Marco

PAGE 4

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

• page 5

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 <-Marco

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 <-Marco

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 <-Marco

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:
• Marcel Martin:
• Andreas Sjo¨din:
• Bjo¨ rn Usadel:
• Matthew Young:
• Eric C. Olivares:
• 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
• Marcel Martin:
• Andreas Sjo¨din:
• Bjo¨ rn Usadel:
• Matthew Young:
• Eric C. Olivares:
• Dan M. Bolser:

Q3

• Dan M. Bolser doesn't have a fax number. Please advise
• Jing-Woei Li, Tel. +852 xxxx xxxx (to be confirmed tomorrow) Fax. Do not have a fax number. Please advise
• Eric Olivares, Tel. Fax.

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/?):

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

Dan: Only Figure 2 cannot be converted to grey scale in it's current form. A grey scale friendly version of this figure could be created upon request (necessitating a minor change to the legend).

Figure 1 and 3 can be converted to grey scale. No changes to the text or figure legend is necessary.

Figure 1 looks much more attractive in color.

Marco:

Figure 1 and 2 cannot be converted to grey scale.

Figure 3 can be converted to grey scale.