https://github.com/mooerslab/manuscriptinlatex
Template for the first submission of a manuscript
https://github.com/mooerslab/manuscriptinlatex
first-submission latex-template manuscript
Last synced: about 1 month ago
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Template for the first submission of a manuscript
- Host: GitHub
- URL: https://github.com/mooerslab/manuscriptinlatex
- Owner: MooersLab
- License: mit
- Created: 2022-09-05T16:23:49.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-03-05T22:57:49.000Z (3 months ago)
- Last Synced: 2025-05-08T01:46:33.216Z (about 1 month ago)
- Topics: first-submission, latex-template, manuscript
- Language: TeX
- Homepage:
- Size: 2.01 MB
- Stars: 3
- Watchers: 1
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://opensource.org/licenses/MIT)
# Generic template in LaTeX for the first submission of an academic manuscript
## Tower of First-Submission Babel
A point of perpetual confusion for me is that the availability of style files for LaTeX for various Academic journals implies that you should prepare your first submission using the official template.
This is not true, and this is much more trouble than it is worth, especially if your manuscript is rejected, as most are.
Journal configurations vary widely between journals: It can be much more challenging to reformat a manuscript than it may appear at first sight.
Instead, you only need to submit your first submission as a PDF.
You could use a format for that first submission that is easy for reviewers to read and edit when printed out.
It should also be simple for you to assemble.
(I know; you could format it for BioArxiv in LaTeX.
This step is part of many people's workflows.)
## Solution: a generic template for the first submission
This GitHub repository is for a generic journal article template (main.tex) that I use to prepare my first manuscript submission as a LaTeX document.
I used one extra file for styling the bibliography, spbasic.bst.
The template includes examples of the following elements:
- figure
- tables
- equations
- code block
- bibtex file
Delete the boilerplate that you do not need and fill out the sections with your amazing results and submit.
## Title page
## Second page
## Compiling in terminal
Must use `-shell-escape` when using the minted package.
```bash
pdflatex -shell-escape main
bibtex main
pdflatex -shell-escape main
pdflatex -shell-escape main
```
## Configuration for using LaTeX with AucTex in Emacs
Add to the init.el file:
```latex
(setq TeX-command-extra-options "-shell-escape") ; required to enable use of the minted package for syntax highlighing of code.
(use-package auctex
:ensure t
:defer t
:hook (LaTeX-mode . (lambda ()
(push (list 'output-pdf "Skim")
TeX-view-program-selection))))
```
### Note for org-mode users
Wouter Spekkink has written a detailed [blog post](http://www.wouterspekkink.org/academia/writing/tool/doom-emacs/2021/02/27/writing-academic-papers-with-org-mode.html) about writing an academic article in org-mode and then exporting it to LaTeX.
## Features
- Running title and short author list in the header of each page ease sorting printed versions when two or more documents have been stored together for editing away from the computer, like during air travel.
- Use a global.bib file rather than bibitems to assemble the bibliography.
- Use the booktabs library for pretty tables even if I have to downgrade them on the final submission with the journal's style file.
- A list of tables is autogenerated.
- Use the graphicx package to import images.
- Support for including figures in an old-fashioned Figure section rather than embedding them in the text. Hyperlinked labels allow you to navigate instantly to a figure. A list of figures is autogenerated.
- Support for including tables in a Tables section.
- Reminders (i.e., remember to spell out the hypothesis in the Introduction) of what should go where in a deletable or foldable comment.
- Support for equation typesetting in a custom environment that supports captions.
- Support for syntax highlighting of code blocks and using captions for each code block.
After your manuscript is accepted, you can reformat it to comply with the Journal's style.
LaTeX template and style files can be found on the Journal's website.
The Overleaf.com site has a gallery of journal-article templates that run on Overleaf.
## Complementary writing tools available at github.com/MooersLab
### Writing Log
See this [site](https://github.com/MooersLab/writingLogTemplate) for a template to organize your thoughts and track your progress on your writing project.
I store the writing log in the same folder as all the files for my writing project.
### Annotated Bibliography
See this [site](https://github.com/MooersLab/annotatedBibliography) for a template to create an annotated bibliography in LateX.
This is an excellent place to store your notes from reading the literature.
I store the annotated bibliography in a subfolder in the same folder as all the files for my writing project.
### Slideshow Template
See this [site](https://github.com/MooersLab/slideshowTemplateLaTeX) for a template to create a slideshow to advertise your manuscript.
### Diary for 2024 in LaTeX
[See](https://github.com/MooersLab/diary2024inLaTeX). Can serve as a template for related purposes.
### latex-emacs
See this [site](https://github.com/MooersLab/latex-emacs) for a latex-emacs configuration file.
This configuration allows you to run Emacs with LaTeX in isolation from your main configuration.
### snippet-latex-mode
See this [site](https://github.com/MooersLab/snippet-latex-mode) for a collection of yasnippet snippets for latex-mode in Emacs.
These extend the default set.
### emacs-quizzes
Improve your recall of Emacs commands in a few minutes a day thanks to spaced repetition.
The [site](https://github.com/MooersLab/qemacs) has a set of fill-in-the-blank quizzes.
### LaTeX in Emacs
Learn how to use [LaTeX in Emacs](https://github.com/MooersLab/BerlinEmacsAugust2022) by watching the slides I presented at the Berlin Emacs Meetup on 31 August 2022.
This talk was not recorded.
### GhostText
Edit text areas in a web browser from your [favorite text editor](https://github.com/MooersLab/DSW22ghosttext).
The text area can be the opened tex file on Overleaf.
This talk was recorded: See the corresponding [video](https://mediasite.ouhsc.edu/Mediasite/Channel/python/watch/4da0872f028c4255ae12935655e911321d).
### The Writer's Law
Some [guidelines](https://github.com/MooersLab/thewriterslaw) to productive writing.
|Version |Changes |Date |
|:-------------|:-----------------------------------------------------------------------------------------------------|:---------------------|
| Version 0.7 | Added badges update table. | 2024 October 11 |
## Sources of funding
- NIH: R01 CA242845
- NIH: R01 AI088011
- NIH: P30 CA225520 (PI: R. Mannel)
- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)