Scrivener for Scientific Writing — setup
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Below please find my final setup for writing a scientific paper/book. Although my requirements seemed to be clear&simple, it took me app. 40 hours to put everything together. And here it is: my final set-up ready :)
My needs
I want my system to support me in:
- Managing scientific sources and citations
- Insert and enumerate simple equations
- Export the final document to MS Word docx format, keeping all Styles (like headings).
Tools
- Storing all documents and drafts: Google Drive
- Managing scientific sources: Zotero (https://www.zotero.org/)
- Making notes and structuring content: MindManager (https://www.mindjet.com/mindmanager/)
- Writing: Scrivener (https://www.literatureandlatte.com/scrivener/overview)
- Exporting: Pandoc (https://pandoc.org/).
My Workflow
Initiate the project
- set-up a Google Drive folder and create subfolders: {book title},… {book chapters}…, setup
- set-up a Zotero folder for all needed resources {book title}
- export this folder to Setup Google Drive folder in a BibTex format using Better Bibtex plugin (how to can be found in points 1–5 here) > mylibrary.bib
- in the Setup Google Drive folder store: a docx template for Your book (with all proper styles), mylibrary.bib and Your preferred citation style (choose sth from https://www.zotero.org/styles, eg. https://www.zotero.org/styles/chicago-author-date-16th-edition)
Managing knowledge sources
- Gather all necessary knowledge resources (books, papers, websites, reports etc.) using Zotero web plugin, it’s ISBN search or just drag&drop files from Your folders
- Organize them using TAGS
- Make notes: annotate PDFs and then export notes to Zotero using ZotFile, integrate the most important notes into MindManager
- Make draft structure (paragraph-detail level) in MindManager
Writing
- organize all the writing in Scrivener using folders
- control targets and writing progress with meta-tags
- compile to docx via MultiMarkdown and Pandoc (see compile presets below).
Install
Zotero
- Install Zotero (from www.zotero.org)
2. Install useful plugins:
- Better Bibtex plugin (see installation instructions here) > to export Your reference library as a BibTex file
- ZotFile > for efficient PDF management, especially exporting annotations from PDF to Zotero
3. Install Zotpick-applescript > for a possibility of calling Zotero citation during writing with a single click:
- Mac-OS only: Create a dedicated app with Workflow Manager (see installation instructions https://raphaelkabo.com/blog/posts/markdown-to-word/)
Scrivener
I suggest to purchase it directly from https://www.literatureandlatte.com/scrivener/overview — an AppStore version has some limitations.
Pandoc
For markdown to docx conversion.
- from the terminal with
brew install pandocor from this page. - Additionally, install the following pandoc extensions
- pandoc-citeproc: for managing citations. Installation instructions here, or:
brew install pandoc-citeproc
- pandoc-eqnos: for enumerating equations. Installation instructions here, or
pip install pandoc-fignos
Setup
The only, and the most difficult to, setup you need is Scrivener.
(suggested, but not required): import my Scrivener preferences and theme settings from scrivener settings GitHub folder
Compile presets. This is the most important — magic happens here!
From scrivener settings import My Markdown.scrformat.
- click File > Compile
- drag and drop My Markdown.scrformat into the Formats panel on the right. Choose “My Formats” option
To see it’s presets: right-click > Edit. I made a lot of changes to Styles, basing mostly on Scrivomatic MarkDown exports (see: https://github.com/iandol/scrivomatic).
The most important settings are in the Processing script. It took me app 30 hours to get there :). When you click Processing > Edit Script you will see sth like that:
The script itself is below (for Your Copy-Paste convenience — some fine tuning will be necessary):
fullfilename=$1
filename=$(basename "$fullfilename")
fname="${filename%.*}"pandoc --filter pandoc-citeproc --filter /Applications/Anaconda/anaconda/bin/pandoc-eqnos --bibliography '/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/mylibrary.bib' --csl '/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/ee.csl' $filename -f markdown-auto_identifiers+tex_math_dollars --reference-doc '/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/MS Word - Cambria.docx' -o $fname.docx
IMPORTANT: update paths to Your local settings:
/Applications/Anaconda/anaconda/bin/pandoc-eqnos <<< Your pandas-eqnos installation. Attention: I don’t know why, but even if pandoc-eqnos works perfect from Your terminal, here the full path is needed…
/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/mylibrary.bib — this is a path to Your Google Drive/…/setup/mylibrary.bib file.
/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/ee.csl — this is a path to Your Google Drive/…/setup/{preferred style sheet} file.
/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/MS Word — Cambria.docx — this is a path to Your Google Drive/…/setup/{preferred docx style} file.
That’s it! It should work, although it may be very cumbersome…
Usage
Create a New Scrivener Project
Write something
Compile:
- Compile for: MultiMarkdown
- Choose Presets: My Markdown
My Example
I put one example on my GitHub folder: https://github.com/wodecki/writing
- Open draft project from the main GitHub folder
- Compile
- And check the output.
Useful resources
My inspirations:
https://raphaelkabo.com/blog/posts/markdown-to-word/
http://davepwsmith.github.io/academic-scrivener-howto/
Zotero, Markdown and Pandoc:
All videos on Zotero, Markdown and Pandoc from Nicholas Cifuentes-Goodbody, starting from https://www.youtube.com/watch?v=Gm2MbYB3k4o&list=PLXt-tu7G1H3vlRXLmGyOzeAp7ZKDK0pty&index=1. Great!
Scrivener has its own really great tutorials here.
My Github project with all the files
https://github.com/wodecki/writing
Happy writing :)
Andy