Hello there bloggies! Welcome to Trainee Tuesday!

The other day I was submitting a paper. As a trainee, it is one of the best feelings. You have done all of your experiments and analyses. Made sure everything is controlled properly. Got these and the paper through all the revisions your PI wanted to make. And finally, circulated and got the okay from all of your co-authors. You are finished!

Well, that is if you can navigate the needlessly complicated manuscript submission system. A system only rivaled in its illogical setup by eRA Commons (the NIH grant submission site). One would think that all you would need to do is upload a word document or pdf of your manuscript and cover letter. What a foolish thought!

Here are some of the most annoying parts of submitting your manuscript (hint, none of these actually have anything to do with writing your paper or with your experiments/analyses):

1) Entering the author information into the submission system

On your title page, you usually the list of authors and their It is fairly easy to interpret. One would think that would be good enough for the editorial office. Of course, it isn’t. You need to individually enter each author, degree, and affiliations into the system. That would be fine, but some journals won’t let you edit the author information if they are already in the system. Even if their affiliations or degrees have changed! Good luck if you are the submitting author on one of this mega-consortia papers with 100+ authors. Maybe in the future you’ll just be able to upload a word document or text file. I wouldn’t think it’d be difficult to read into the system. Or maybe I’m hoping for far too much.

2) Every journal has their own way of citing references in the text and formatting the reference list.

For some reason, every journal has decided to handle references in their own special way. Some like you to number them in the order they appear. Others want to use the first author et al. year published (e.g., Smith et al. 2001) and have the references listed in alphabetical order. In the reference list, some want periods after each initial, colons after issue numbers, or other random punctuation marks. I don’t get it! The point of having a reference list and citing references in your paper is to show evidence for your assertions and conveniently list these for the reader. That way the reader can easily find the relevant paper if need be. No one cares about numbering and punctuation markers. The reader just needs to be able to find the right paper!

PS Learn EndNote or RefMan early on. I wrote a review with over 150 references. All done by hand. I teetered on the edge on sanity.

3) Uploading figures and tables

Figures and tables are probably the most informative parts of your manuscript, other than the methods. A large number of journals require that figures and tables either be uploaded separately or placed at the end of your manuscript. This is usually done to make sure the figures are of high enough quality for publication. But, this puts the figures and tables are at the end of the manuscript as far away from the text citing these figures/tables as possible. Reviewers are thrilled at the prospect of flipping through dozens of pages trying to match the correct figure/table to the right bit of text. I know I have never been incensed flipping around a stack of 50 pages trying to interpret a complex figure. Let the submitting author embed tables and figures within the text during the first rounds of review. Worry about figure quality later if/when the prospect of publication is more realistic. As long as the figure is readable, the reviewer can do his or hew job.

Nonetheless, submitting a paper is a fantastic accomplishment and feeling for any trainee. The process could be vastly improved, but take some time to congratulate yourself. It is quite a feat.

Thank you for dropping by Trainee Tuesday! What annoying things have you noticed about submitting a paper? Comment below or on twitter @DrFsThoughts. See you tomorrow!

-Dr. F

PS It’s snowing again here. Grrrrr…