Cite-while-you-write (CWYW) with Zotero

Cite-while-you-write (CWYW) is the important step in academic writing. A good setup can make writing with Markdown and formatting with Marked 2 app much more rewarding.

Steps:

• Write with Zettlr
• Write with other editors (macOS)
  • Zotpick.applescript by davepwsmith
  • ZotHero via Alfred

Export with Marked 2 app

To share my writing with others, I use Marked 2 app (macOS) to convert the Markdown files into other formats, such as PDF or DOCX.

TL;DR:

1. Configure Marked 2 to process citation in markdown files (.csl)

   Marked 2 App -> Preferences -> Advanced Set Path to:

   /usr/local/bin/pandoc
   

   Set Args to:

   -f markdown+smart -t html5 --filter=/usr/local/bin/pandoc-citeproc --bibliography ~/Zotero/Library.bib --csl ~/Documents/Zotero/Pandoc/CSL/amj.csl
   

2. Preview/drag&drop markdown files in Marked 2 app

3. Choose the styles for the document (.css)

4. Export to PDF, DOCX, or HTML

Configure Marked 2 App

You need:

• Zotero with BetterBibTex
• Pandoc and pandoc-citeproc
• Citation Style Language (CSL) file for the reference style of your choice. Preview and download at the Zotero Style Repository.

Select Document Style

• Marked 2 converts a Markdown file into HTML document file, which in turn gets formatted according to a chosen CSS template
• CSS is a language that describes the style of an HTML document

Choose the Right Style:

• Marked 2 has a Style Gallery. I have contributed a template (Chicago Academic) based on the Chicago Manual of Style.
• Additional CSS templates I created for academic writing:
  • Chicago Academic.css: based on The Chicago Manual of Style
  • AMJ Academic.css: based on the Academy of Management Journal Style Guide
  • Academic CV.css: suitable for both academic and industry CVs
  • Academic Review.css: based on Academy of Management's Reviewer Guidelines

Print and Share

• To PDF: Marked 2 supports direct export to PDF format; alternatively, export to HTML format and print from your browser
• To DOCX: export to HTML format and open/save to DOCX format in Microsoft Word

Issues and Limitations with Marked 2

Marked 2 app has issues with exporting files into Word documents. The formats defined by CSL files can be lost.

• Solution 1: Export to HTML files, then open with Word
• Solution 2: Use DocDown by Ralph Kabo

DocDown: Alternatives to Marked 2

• Download via GitHub
• "Takes Markdown files, filters them through a Zotero bibliography file, a CSL file, and a reference .docx file, and exports a Word document with embedded citations and styles."
• About DocDown
• Set your own workflow from markdown to docx