paper template

LaTeX template for scientific paper. Includes examples of bibliography, and figure / table references to a supplemental file. The main document is manuscript.tex. The supplement.tex document is where you can create a supplemental information document. The template uses only Latex-built-in classes and styles. Many journals define their own templates, document classes or citation styles.

On Overleaf, the cross-referencing between main and supplement document needs some extra fix to make the compilation work (https://www.overleaf.com/learn/how-to/Cross_referencing_with_the_xr_package_in_Overleaf) which is the purpose of the latexmkrc file.

Commandline usage:

• compile.zsh compiles manuscript and supplement document to PDF.
• clean.zsh removes lots of temporary files that are produced during the compilation.

Local setup:

(1) You need TexLive to compile the document. On OSX, the full package can be installed with homebrew:

    brew install texlive
    brew install biber

(2) The compile and clean scripts assume you have zsh installed (alternatively, replace the zsh command within the script by bash):

    brew install zsh

(3) It's a good idea to track the project on github. Install git with homebrew:

    brew install git

• copy the template repository into a new repository on github
• then create a local copy: git clone http://... (the link is displayed in the repo page on github)

Overleaf & Github

This is a more advanced but IMO the most elegant setup. You first "fork" the template into your own github repository. Then you create a new Overleaf project from that repository. This later allows you to push changes back to github. It also allows you to create a local copy of the manuscript folder on your computer, to edit it there and then to push those changes back to github and from there to overleaf.

(1) Go to: https://github.com/strubelab/paper_latex_template

(2) Click "Use this Template" and then "create new repository"

• Note: You need to have a github login for this to work. Create the repository within the strube organization if you want to give immediate access to lab members.

(3) Import manuscript repository into Overleaf

• Log into Overleaf (use KAUST email to benefit from Premium features)
• New Project / Import from Github
• Note: if you do this for the first time, follow the instructions to link your Github account to your Overleaf account
• Select the new repository as a source

You can now edit the project as usual in Overleaf. Once in a while, you can sync changes back to github:

• Go to "Menu" / "Sync" and select "Github"
• Pull changes from github first
• Then Push Overleaf changes to the github repo

For working on a local copy, git clone the github repo and then use git pull, git add and git push to sync local changes back to github. Then use the sync button in Overleaf to merge these changes back into overleaf.

Overleaf without Github

This creates an overleaf project that is not linked to any github repository.

(1) Download the template into a new folder on your computer

(2) In Overleaf, "New Project" / "Upload Project"