NAR Paper

Overivew

The Nucleic Acids Research (NAR) paper in the annual database issue presents to the world our latest data and software developments. There is a long history of different authors and this page provides a place to find resources regarding the process.

NAR provides many instructions for writing the paper, important to review. A template is provided at this link.

NAR provides a Checklist and a Revision Instructions Sheet after you submit your paper, but review them first to help you write your first drafts better.

Presentations

Cath wrote the paper in 2016 (2017 Update is submitted in Sept. 2016) and put together a "Reflections: Writing the NAR" presentation with slides available here.
- You will want to keep Cath's slides handy, the presentation is packed with information.
Jairo wrote the paper in 2020 and put together a "Writing the NAR Update" presentation with slides available here.
BrianL wrote the paper in 2021 and put together a "Writing the NAR Paper" slide deck available here.

Tips

Cath's tips seem pretty timeless for any potential NAR author.

Schedule

Here is a model reverse timeline schedule from June to Labor Day. Note how it takes into account planned vacations to frame things in a realistic context.

Week end 9/Z: (9/15 Due)
Week end 9/Z:  (Labor Day Holiday)
Week end 9/Z:
Week end 8/Y: FINALIZED DRAFT TO ENTIRE TEAM
Week end 8/Y: 
Week end 8/Y:  DRAFT2  REVIEW TEAM_2
Week end 8/Y:  (Vacation_2 if planned 8/A-8/B)
Week end 7/X:  DRAFT1    REVIEW TEAM_1
Week end 7/X:  
Week end 7/X: (Vacation_1 if planned 7/A-7/B)
Week end 7/X:  (4th of July Holiday)
Week end 7/X:  (Last week of June)

Outline

Here is a conceptual skeleton outline to help launch things.

ABSTRACT
INTRODUCTION
NEW DATA IN THE GENOME BROWSER
-subsection 1
-subsection 2 
-subsection 3 - as makes sense
NEW SOFTWARE FEATURES IN THE GENOME BROWSER
-subsection 1
-subsection 2
-subsection 3 - as makes sense
FUTURE PLANS
OUTREACH AND CONTACT INFORMATION
ACKNOWLEDGEMENTS
FUNDING
REFERENCES

Here is a list of all previous outlines for ideas.

References

There is an internal wikipage about using Zotero that can be helpful for references. It turns out you don't want to use the "NAR Web Server Issue" in Zotero style that adds URLs.

Images

If you have screenshots will likely need to correct the DPI (as mentioned in Cath's overview). One tool to try is GIMP (https://www.gimp.org/) to do the conversion. Another is online at https://convert.town/image-dpi.

If you upload your images to Dev you can run a program that is already installed called imagemagick invoked with the "convert" command to take an input "image" and output a "resultImage" to 300dpi and in the process make a very nice resample so it looks the best possible: convert -units PixelsPerInch image -resample 300 resultimage

Real example commands involving 7 image files called FIGURE_#.png with results placed in a created now300DPI directory:

scp FIGURE_* login@hgwdev.gi.ucsc.edu:/cluster/home/userName/public_html/location
for i in {1..7}; do convert -units PixelsPerInch FIGURE_$i.png -resample 300 now300DPI/FIGURE_$i.png; done

Previous NAR papers

Referees aka Reviewers

Cath's PDF presentation is chalk full of resources to google docs. We have been recording the referees used here, please help future NAR authors and list the ones you use. Email the group to ask for ideas of good names (some people have recently acted as a referee on a paper for others in the field and they might suggest new names). You will also find in Cath's PDF presentation answers to other google docs like one modeling the "extended abstract" submission that occurs only after your paper is accepted.

Responding to Referees

You want to include a wide range of the top paper authors regarding the content of the feedback. Cath's PDF presentation provides a google doc link of a very nice model of how she handled resourcing input. One mode of responding is reply in red text with an opening paragraph thanking the reviewers for their assistance improving your manuscript. Then place their bullet point items inline in normal black text and respond to each one by one in more red writing (this is to match how any changes to your manuscript will be in red writing, which you will note as you reply to their points, "The section titled X is now revised with Z and Y" where track changes in MS Word have made your changes red.).

License charge

To publish the paper in the past a PO (Purchase Order) was required, you want to contact GI Finance (genomics.finance@ucsc.edu) to communicate about the need to pay for the publication. In 2021 the PO process changed. In the past we have used the "CC BY" which is explained at NAR: The Creative Commons Attribution licence (CC BY) is the most liberal of the Creative Commons licences and allows for unrestricted reuse, even commercial, as long as the author is credited for their original creation. While Oxford Journals Author Services allows you to pay online using a credit card, our grant and finance pays for this transaction (don't ask ProCard holder for the Browser credit card number). The old PO way for this charge was $1,385 USD in 2016 and $3,800 USD in 2020, so don't be surprised if it is a lot more in the future. In 2021 finance informed BrianL that in stead of a PO we can "Just send the invoice to [Finance] and I [Linda Knipe] will submit for direct payment to the vendor." This should make things easier as the PO process was a bit complicated previously. Odd note, this step requires a separate account on the Oxford site.

Final Revisions

You will get queries on items to respond to (like, ensuring you double-check the names and the references). Here's the FAQ and the answer to How do I answer author queries? Author queries will be highlighted as yellow boxes in the text. To answer them simply type your answer into the text next to them in bold. In reality, you click into the yellow query box, and then a "Reply" pop-up will show, and then you can paste your response into that pop-up and it will end up being highlighted as well.

NAR Paper

Contents

Overivew

Presentations

Tips

Schedule

Outline

Here is a list of all previous outlines for ideas.

References

Images

Previous NAR papers

Referees aka Reviewers

Responding to Referees

License charge

Final Revisions

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