NAR Paper

Overview

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.

The NAR deadline is September 15th and the instructions for writing the paper can be found at this link.

An email to request to submit the NAR paper is sent to the NAR Executive Editor, Daniel J. Rigden. Previous emails can be found at this link. A template of the NAR paper is provided at this link.

The NAR paper is submitted here. A head start with familiarizing with the NAR website is recommended.

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 10/Z: Check proof
Week end 10/Z: Pay license for article 
Week end 10/Z: Submit the revised version of the manuscript 
Week end 10/Z: Address feedback from reviewers 
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: Finalized the author's list
Week end 8/Y: First pass before sending it around
Week end 8/Y: (Vacation_2 if planned 8/A-8/B)
Week end 8/Y:
Week end 7/X: (Vacation_1 if planned 7/A-7/B)
Week end 7/X: (4th of July Holiday)
Week end 7/X: Start filling in details for the report
Week end 7/X:
Week end 6/X: Send email to request to submit the NAR paper

Make sure that the last author has read the full paper. Remind him or her and bug them at will :-) until you get the go ahead for submission, since the last author is (supposedly) the one who is the one who is responsible for the content with the editor and w/r to NIH...

Getting the finalized list of authors sooner rather than later is recommended. You will need the author's list to get the information for the funding section. The funding section will require emailing Greta (gretamartin@ucsc.edu) with the author's list.

Outline

Here is a conceptual skeleton outline to help launch things.

ABSTRACT
INTRODUCTION
NEW AND UPDATED ANNOTATIONS
-subsection 1 (New clinical tracks)
-subsection 2 (Gene set updates)
-subsection 3 (Other new tracks)
-subsection 4 (New hubs)
...
NEW GENOME BROWSER SOFTWARE
-subsection 1 (New hub features)
-subsection 2 (New and updated tools)
-subsection 3 
...
FUTURE PLANS
DATA AVAILABILITY
ACKNOWLEDGEMENTS
FUNDING
REFERENCES

Here is a list of all previous outlines for ideas.

You may also want to look at the previous NAR submission on the https://mc.manuscriptcentral.com/nar website. The submission can be accessed from the Author tab, and the View Submission link will be under the paper's title.

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.

You will be required to upload a graphical abstract. The graphical abstract in past submissions has been an image of hgTracks. Technical Requirements:

Size: 5x2 aspect ratio, 127x50mm or 5x2in minimum
File type: TIF, EPS or editable PDF (MP4 for videos)
Resolution: 300-600dpi minimum
Orientation: landscape
Font: Use a sans serif font such as Arial, 12–16 points

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.). You may also want to look at the previous NAR Revised submission on the https://mc.manuscriptcentral.com/nar website. The submission can be accessed from the Author tab, and the View Submission link will be under the revised paper.

Nucleic Acids Research: check your proof

You will get an email to review the manuscript proof. You may want to review their FAQ page on how to respond or enter your corrections to the manuscript: https://powerxeditor.aptaracorp.com/oup/UserDocument/QRG/General-PXE%20FAQ.pdf.

License charge

You will get an email after the paper has been accepted about selecting a license for the article. Forward the "Please select a license for article" email to the project manager (Clay Fischer) and the Financial Services Specialist (Linda Knipe) for approval. You can find the Financial Services Specialist information info at https://businessoffice.soe.ucsc.edu/directory. We select and agree to the Open Access CC BY License option. Select third-party contact for the payment. The third-party contact would be the Financial Services Specialist.

After publication: Add a link to the paper from our webpage

Once the paper is published, update this page: https://genome.ucsc.edu/cite.html and replace the PMID and DOI on this page with the new one.

NAR Paper

Contents

Overview

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

Nucleic Acids Research: check your proof

License charge

After publication: Add a link to the paper from our webpage

Navigation menu

Page actions

Page actions

Personal tools

Genecats Wiki Navigation

Search

Media Wiki Navigation

Tools