Tag Archives: manuscript

Manuscript Re-submission – Oly Stress Response to PeerJ for Review

Last August, we made our initial submission of this paper to PeeJ.

Today, we re-submitted the revised manuscript.

The repo for this paper is here.

I’ve also submitted an updated pre-print. I will update this post when it is publicly accessible (it has to be approved by PeerJ staff before it becomes public).

UPDATE 20170703 – Updated pre-print is now available: https://peerj.com/preprints/1595/

Goals – June 2017

Well, my previous goal was to tidy up an existing manuscript and get it re-submitted to PeerJ. That’s pretty much done, as Steven will be giving a final once over and formatting the rebuttal letter prior to resubmission.

June will be a bit of a short month for me, due to some travel, but here’re some things on the agenda:

  • Update the Oly Genome Wiki to accurately reflect the most recent PacBio Sequencing we had done.

  • Related to the above goal is updating Nightingales to house just the raw sequencing data files for the Oly PacBio sequencing, while archiving the associated meta data (QC files, reports, etc).

  • Related to THAT goal is then updating our Nightingales spreadsheet to reflect, and provide links to, the raw sequencing files.

  • Establish (and build out) an “On Boarding” repo in the Roberts Lab GitHub Page. This should make it easier for new lab members to find the various resources they need. More importantly, it should make it easier for us to direct people to find that info!

Manuscript Writing – Submitted!



Here are some useful links:

data records repo-URL: https://osf.io/j8rc2/
draft repo-URL: https://github.com/kubu4/paper_oly_gbs
draft: https://www.authorea.com/users/4974/articles/149442
preprint (Overleaf): https://www.overleaf.com/read/mqbbvmwxhncg
preprint (PDF): https://osf.io/cdj7m/

Manuscript – Oly GBS 14 Day Plan

For Pub-a-thon 2017, Steven has asked us to put together a 14 day plan for our manuscripts.

My manuscript is accessible in three locations:

Current: Overleaf for final editing/formatting before submission Scientific Data.
Archival: Authorea for initial writing/comments.
Archival: GitHub for initial writing/issues.

Additionally, I have established a data repository with a Digital Object Identifier (DOI) at Open Science Framework

Here’s what I have going on:

Day 1

  • Convert .xls data records to .csv to see if they will render in OSF repo.
  • Assemble figure: phylogenetic tree.
  • Add figure to manuscript.
  • Deal with any minor edits.

Day 2

  • Assemble figure: Puget Sound map.
  • Add figure to manuscript.
  • Deal with any minor edits.

Day 3

  • Submit? Depends on what Steven’s availability is to finish of Background & Summary and write up Abstract.

Manuscript Writing – The “Nuances” of Using Authorea

I’m currently trying to write a manuscript covering our genotype-by-sequencing data for the Olympia oyster using the Authorea.com platform and am encountering some issues that are a bit frustrating. Here’s what’s happening (and the ways I’ve managed to get around the problems).



PROBLEM: Authorea spits out a browser-crashing “unresponsive script” message (actually, lots and lots of them; clicking “Stop script” or “Continue” just results in additional messages) in Firefox (haven’t tried any other browsers). This renders the browser inoperable and I have to force quit. It doesn’t happen all of the time, so it’s hard to pinpoint what triggers this.



SOLUTION: Edit documents in Git/GitHub. I have my Authorea manuscript linked to a GitHub repo, which allows me to write without using Authorea.com. This is how I’ll be doing my writing the majority of the time anyway, but I would like to use Authorea.com to insert and manage citations…



PROBLEM: Authorea remains in a perpetual “saving…” state after inserting a citation. It also renders the page strangely, with HTML <br></br> tags (see the “Methods” section in the screen cap below).


SOLUTION: Type additional text somewhere, anywhere. This is an OK solution, but is particularly annoying if I just want to go through and add citations and have no intentions of doing any writing.



PROBLEM: Multi-author citations don’t get formatted with “et al.” By default, Authorea inserts all citations using the following LaTeX format:


Result: (Elshire 2011).

This is a problem because this reference has multiple authors and should be written as: (Elshire et al., 2011).

SOLUTION: Change citation format to:


Other citation formatting options can be found here (including multiple citations within one set of parentheses, and referring in-text author name with only publication year in parentheses):

How to add and manage citations and references in Authorea



PROBLEM: When a citation no longer exists in the manuscript, it still persists in the bibliography.

SOLUTION: A known bug with no current solution. Currently, have to delete them from the bibliography by hand (or, maybe figure out a way to do it programatically)…




PROBLEM: Cannot click-and-drag some references from Mendeley (haven’t tested other reference managers) without getting an error. To my knowledge, the BibTeX is valid, as it appears to be the same formatting as other references that can be inserted via the click-and-drag method. There are some references it won’t work for…


SOLUTION: Use the search bar in the citation insertion dialogue box. Not as convenient and slows down the workflow for citation insertion, but it works…