News and Views from a Mass Spectrometry Lab in Irapuato, Mexico

Academic writing: docx, LaTeX or markdown?

Today I wrote my productivity report for 2019. Of course, I was using the official .doc (!) format of our institution. As well, I wrote four letters with my .docx and .odt templates. Word (https://products.office.com/word), LibreOffice (https://www.libreoffice.org/) and similar "What You See Is What You Get" (WYSIWYG) word processors are ideal for quickly creating simple documents.
However, for scientific manuscripts or dissertations, you can use more advanced programs. The reference for academic typesetting is LaTeX (https://www.latex-project.org/). Writing a text is somehow similar to programming, and the produced PDF files are ready to publish. However, little errors, such as a forgotten '}' may cause hours of bug hunting and drive away beginners. Online services, such as Overleaf (https://www.overleaf.com/) greatly facilitate the use of LaTeX and collaborative working. LaTeX is the first choice for people who aim towards correctly set equations and beautiful outcomes.
In the last years, writing texts in markdown is becoming increasingly popular. The plain text files contain only a few special commands that define the structure, such as '#' for a section heading, or formatting, such as '**' for bold text. Thus, the syntax is easy to learn, and the files can be opened with any text editor. There are exclusive markdown "What You See Is What You Mean" (WYSIWYM) editors such as Ghostwriter (https://wereturtle.github.io/ghostwriter/), but also working with more nerdy editors such as Atom (https://atom.io/) or Vim (https://www.vim.org/) is possible. Several programs already provide exporting the markdown text to docx, odt, html or pdf. Pandoc (https://pandoc.org/) enables the use of custom templates, e.g. the latex or docx style templates of journals. Markdown files are very light-weight, cross-platform compatible and mobile-friendly.
If you are interested and look for more information:
Krewinkel A, Winkler R. 2017. Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. PeerJ Computer Science 3:e112, https://doi.org/10.7717/peerj-cs.112

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