Please consider writing your doctoral thesis using LibreOffice. When writing and citing is complete and final (and you have removed the field codes) only then use Ulysses to refine and dress-up your manuscript.

Thanks, Adam and DWL. I will look into LibreOffice and the ODF scan, but just to clarify: Ulysses is for writing many many words of semantically structured text, not for polishing the looks of a manuscript. That's for later.

Please explain why the RTF scan would be unreliable. Does it simply not scale well?

Thanks again for your comments.

I'm simply recommending that, when working on something as important as a doctoral thesis, that tried and true software be used.

I have used Ulysses (the current and an earlier version). I like it better than Scrivener although Scrivener is clearly more powerful. However, for a critical document that is likely to undergo multiple major revisions including moving large blocks of text, the risk of scrambling citations and bibliography entries are higher with these. I speak from experience as an adviser of grad students who have attempted writing their theses with these advanced tools. The prevalence of problems is more than 50% with Scrivener while with conventional word processors is no more than 10-15%.

I make no argument that one should have the freedom to choose the software that works for them. I still say that for what is perhaps the most important document of one's life, it is prudent to use something that has been well-tested and with which the writer has had much experience.

Sebastian, I greatly respect your mind as a coder. I don't know the software you used to write your dissertation. However, you and Frank Bennett, are not typical writers. I believe that the typical writer of a thesis is more likely to need to think more about the topic and citing authority than the process of writing.

Writing with Ulysses III is a splendid experience. I have memories of what was good about WordPerfect when it was DOS and worked with Reference Manager. However, it is to me what it claims to be -- a tool for creative writers. It is not designed for academic writers. The multiple step process required -- exporting in (questionable) RTF, importing and converting to ODF, and then going back to Ulysses -- provides opportunities for errors and nightmares.

Thank you, all, you've been very helpful. I see the value of the ODF Scan approach, even if until now my testing of the RTF Scan didn't reveal major weaknesses. My field is philosophy and my dissertation will concentrate on a relatively small number of sources, which perhaps makes the ODF route less of a necessity. But being able to add text like "See also" and "chapters 3 and 4" to a citation is a boon, to be sure.

The Ulysses III developers seem to be considering Sente support. I hope to convince them to look into Zotero first. Ideally, UIII would "package" the ODF Scan markers, like URLs and footnotes are now "packaged", in nice little softly coloured buttons hiding ugly markup while showing what's essential, in this case author and year, and .odt would be added to the list of supported export formats.

(In the very best of all possible ideal worlds, inserting citations would be a matter of a keyboard shortcut causing a floating window populated by available sources to appear. Type the first few letters, click, done. Many use UIII full-screen, so dragging citations in or even selecting them in a different application would mean stepping out of the distraction-free environment... Dangerous! Anyway, one can dream.)

I am in a similar position. I'm also a philosopher. rhvdg, let me know if you've made much progress on this issue.

I've spent days trying to figure out a way to use Ulysses and Zotero together. Best I can come up with is... can't really.

I basically write in MD using my own made-up cite keys in the text. Then when draft is done, I export to get manuscript into Word, and then change out citations one-by-one using the Word plugin for Zotero... then generate Reference list.

Yuck.

Which there was something like ZotQuery that was just a tad more user friendly for non-programmers. the Alfred app plus power pack is a lot of $$ to get into to just try out Zotquery. I can read that ZotQuery will produce an alphabetic list of works cited by basically spitting out a Zotero collection, but can it do the equivalent of the RTF scan and produce a reference list in order of cited and re-write cite key with numbers as per style required?

I am hungry to try pandoc, but the command line only interface is intimidating to me. Waiting for a nice GUI with switches and input/output options...

Honestly, the terminal isn't as scary as you might think, and you certainly don't need to be a programmer (see this tutorial and this for basic information). It allows you to accomplish a number of things much more efficiently, and opens up an entire world of small, useful utilities. Many of these (including pandoc) can be installed very easily on the Mac using Homebrew. (For instance, to install pandoc and its citation processor, you simply type 'brew install pandoc-citeproc', and it takes care of the rest.)

That said, yes, it would be nice to have a Markdown editor that also acted as a graphical interface for Pandoc (and, of course, included a version of the Zotero word processor plugins that would insert a citation key). Still, TextMate or even TextWrangler allow you to do much more than you can with a typical word processor.

The wonderful thing about the combination of pandoc and Zotero is that it's the first usable option I've found for doing writing that is truly portable, and allows me to focus on the writing rather than its formatting, which (as I have learned the hard way) publishers just don't generally care about, but they often do have specific requests for providing your text in a specific format (usually Word), and pandoc makes it extremely easy to provide whatever is needed. It's also been really useful for teaching, since I can make up a handout (e.g. collection of a primary source texts) and give students a PDF and EPUB version (which students have really appreciated) from a single source, plus make up slides from it (using pandoc's export to reveal.js format) by simply adding a few horizontal lines.

The other great thing about working in plain text is that it allows you to use a version control system, which (despite their typical limitations for writers) I find is both a very nice way of keeping track of what you're doing with a specific writing project and a great way of managing revisions without having to keep multitudes of old files.

There's all sorts of other information about this online; this post by W. Caleb McDaniel is a good introduction.

What do you mean by reference list? pandoc/citeproc-hs will automatically generate reference lists for items cited in the text, so no need to have a special way of doing that.

If you just want a reference list you might as well do it in Zotero, and create it as RTF or html, no? If you_really_ want it in MD, you can generate it in html and have pandoc convert it to MD, but I don't really see why that would be of interest to anyone.

@dunning - I'd be curious what you use for the citekeys, too.

this is all brilliant.

Thanks @adamsmith. I guess I will read more on how to generate the reference list using pandoc. You're right, no need for it in the MD stage.

@dunning, came across zotxt today as well and intimidated with install and usage. Will push to try it out.

excellent coverage of this... thanks.

I feel like I've come a long way, but now facing a mile of Python errors on first run of Pandoc. May need to bench this and circle back in a few days.

I'm a bit late to the discussion, but I would like to share how I use Zotero and Markdown/Pandoc in Windows (it is useful for Mac users too I believe). The zotxt approach sounds great, but using pip to install packages is just a pain in Windows (at least I gave up on it).

My solution is to use Better Bibtex (https://github.com/ZotPlus/zotero-better-bibtex) and Zotero autoexporting (https://addons.mozilla.org/en-US/firefox/addon/zotero-bib-autoexport/).

After installing Better Bibtex, go to its preferences and set the following citation-key format: [auth][year][Title:skipwords:select,1,1:capitalize:nopunct]

This imitates the citation key system of zotxt using authoryeartitel (everything uppercase), which I find easy enough to remember and still unique enough to identify the items I cite. With Zotero autoexport I regularly update a Bibtex file containing my whole library.

In my writing, I use Pandoc's citation syntax together with my citationkey. When I'm done writing and ready to export, this is my workflow:

- open the folder with your writings (a good folder structure is king when you write with markdown)
- hold the shift-key and right click in the Explorer. This gives you the "Open command window here" option in the right-click menu
- use pandoc with the --bibliography command, like this (here your bib-file is in your documents folder):

pandoc markdownfile.md -o markdownfile.docx --bibliography C:\Users\<Username>\Documents\Library.bib

Also, when you use Windows, there is only one editor that I found really suitable for writing: Sublime Text. Just forget about the rest. Here is a great manual for how to set up Sublime Text for Markdown editing: http://plaintext-productivity.net/2-04-how-to-set-up-sublime-text-for-markdown-editing.html

Edit: I updated the citation key format for Better Bibtex. And good news: The newest version of Better Bibtex updated drag and drop citations for Pandoc, just select 'Pandoc Ciation' in Preferences -> Cite

You're welcome, @dunning, glad you found it useful and thanks for sharing your modification. Personally, I don't like the colon in the zotxt citation key format, which is why I didn't include it.

Meanwhile, I found another great Sublime Text plugin that makes my system more comfortable to work with: Citer (https://github.com/mangecoeur/Citer). It provides citation search and Tab-completion for citations stored in a bibtex file. Inserting citations in plain text Markdown is now just as comfortable as in Libre- or MS-Office (with the Zotero plugins).

Word integrates with Zotero with the elegant Zotero button that appears within the Word software: click the Zotero button while working in Word, choose the reference, click, and the footnote is added and the bibliography updated. When will there be something as elegant for Ulysses?