Markdown, Academic Writing and Reference Management – Looking for an app

First of all hello to the MPU community, it surely looks like an inspiring place!

Regarding my topic: For academic writing I right now use a combination of DevonThink, Zotero and Word (with the Zotero-Plugin) on my Macbook. It works fine and the cite-as-you-write workflow is comfortable. For non-academic writing I’ve looked into markdown and really like the approach. I would like to make use of markdown for academic writing too. Adding to this, I’m looking into switching to a iPad centred Workflow.
Now here comes the question/issue: I know of Workarounds which aim to solve reference management on the iPad, but it’s still not really what I am looking for. Is there maybe a markdown editor for iOS supporting reference management, either with the Zotero API or at least in the form of bibtex files? I know of some LaTex editors for iOS or the web (such as Overleaf) with Zotero integration, but to my knowledge there is no markdown editor with proper reference management. Is this correct? If so – why? Shouldn’t it be quite simple to implement with the Zotero API?

I’m looking forward to comments and suggestions :slight_smile:


I haven’t found what you’re looking for either. Reference management and markdown just don’t seem to go together, regardless of the platform.
I’m back to Texpad now. It provides markdown support, but not that I can see for references. It does work well with Bookends on my Mac, and I’m just going to use LaTeX. Tired of trying to find simpler ways of doing this. I’ll just get better at doing it this way.
Plus you can’t beat the looks of a document created with LaTeX.

Thanks for the input! Did you also try the Texpad iPad app? I might go down this route too, also am considering Overleaf because of its Zotero integration.
Still I think it’s kind of mind-boggling that there seems to be no iOS app with real, non-hacky, cite-as-you-write support after 8 years of iPad.

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Have you looked into Pandoc at all? If you use BibTex references and Pandoc you might well get somewhere when it “compiles”.

Yes, I’m aware of Pandoc.
What I’m missing is an (iPad) App which offers a nice and convenient way of inserting the citekeys (meaning access to my zotero account, a nice picker for the citation, maybe an overview of all citations in one document).
Besides that, am I right that when using a citation Workflow based on Pandoc one needs to “compile” the final Document on a Mac/PC? I’m basically dreaming of an iOS App for academic writing, Markup based with support of reference Management and with the ability of outputting the final PDF (any Devs around here? :wink: ).

While we’re at it, figures with captions and autonumber and reference to the figures, like LaTeX’s \cref{fig:myplot}, and the ability to have subfigures so we can do two or three across…

Well, basically Texpad and LaTeX :slight_smile:

If there are devs listening, I’m sure there are tens of dollars to be made on such an app. Tens, I tell you!


What!? Are you saying that you are willing to spend the other $5 to balance my equal investment?

Sounds like we have a trend. :slight_smile:

In all seriousness, I suspect the path to create an iPad markdown editor with full built-in bibliography support to existing bibliography databases is a long and tortuous one.

I think the best you might find at the moment is a good (markdown) editor and a good citation manager that work nicely side-by-side in split view.

I believe that any markdown with automatic bibliography management will end up converting the document to LaTeX first since the parts are all in place in the latter but need to be built in the former.

Have you considered Scrivener for the non-academic workflow?


I actually have some Shortcuts which work with the Zotero API Auto copy citation references. If you think they’d be useful for you I can write them up.

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There’s also a lot you can do with Editorial & python…

Bookends works well with Ulysses. See this helpful guide: Tutorials - Add Citations to Your Texts: Reference Managers

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Have you considered using Bookdown? It is package for the R language (best known for data munching and statistics) that can generate PDF/ LaTex/ HTML/ e-Pub etc from a single Markdown text file. It has markdown syntax extensions for citations and bibliography. You will need a mac or PC (Windows or Linux) to run R-Studio to generate the actual output, but the input files are plain text, so can be edited with any iOS text editor. I put them in Dropbox for cross platform access, but iCloud should be fine for a pure Apple solution, and edit them with Byword.

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I’ve tried Scrivener but it’s not really what I need – neither for academic, nor for non-academic writing.
You’re probably right with the suggestion of a markodwn editor side-by-side with a citation manager for the moment. At least Zotero annouced that they will develop an iOS app. Still I hope one of the many markdown editors will implement support for Zotero in the future…

This sounds goood – If you don’t mind sharing them/writing them up I would be glad to have a look at them :slight_smile:

I already thougt of that…might have to take another look at Editorial.

I know R (never really used it though) but never heared of Bookdown. Will have a look at it…I’m not sure what “syntax extension for citations and bibliography” means in this case. Do I have to use citekeys while writing (using an iOS text editor) which will be “rendered”/compiled to the actual citations later using Bookdown?
The thing is that I don’t really want to make my writing process more complicated (writing on one device, “compiling” on another). But maybe the solution I’m looking for ist just not there yet on iOS at the current time.

FYI I’ve read that some people on Macs use an Alfred workflow with Zotero - Zotquery:




Also, I found this Zotero-Ulysses usage to be interesting…


Zotquery is no longer developed as the author has left academia, but there’s a replacement Alfred workflow called Zothero - you can find details in the Alfred forums.

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Hello – many reference managers will allow you to export formatted citekeys that you can then paste anywhere you want. The problem is that you will need you Mac to generate the list of references. I personally only use iOS apps for short form writings that do not include complex citations.

The only possible contender that is close to being a workable solution is the brand new text editor Strike (iOS and Mac), which is optimized for collaborative writting. While it is still just a 1.0 version, it looks very promising. If enough of us request this features (I did last week), I think that the developper may be willing to find a way to implement it.

In theory you could use Scrivener on iOS, use citekeys, and write in markdown. You will however need to export/compile your work to generate your reference list in a different editor (e.g., Word, Mellel, Nisus Writer Pro) because Scrivener is not set up to do this natively on iOS or Mac.

The problem I have with Overleaf and other Latex-based online writing softwares is that most of your colleagues will bluntly refuse to work on these platforms.

The combination Mellel 4 and Bookends 13 is really awesome on the Mac. This is my current set-up, and has been now for > 5 years. The two developpers work closely to integrate the softwares seamlessly. The combination Mellel 4 and Bookends 3 works ok on iOS. The newest version of Mellel is able to red comments/track change from Word documents, which is very convenient since most of the world still uses this text editor and is not interested to change. The only issue is that you have to remember to always unscan your manuscript before sharing it if you want to re-import it natively and re-activate the reference citekeys.

The newly released Nisus Writer Pro 3 is actually quite good too.

Another interesting combination if you need to do collaborative writing is Google docs + reference manager paperpile.

If you are into markdown and do scientific presentations, you should definitely check out Deckset 2 ( It works particularly well with Sublime Text when you use this plugin ( You can use citations within slides using the notations [^x] in the text and [^x]: reference details. You can use MathJax for equations too.

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Check this link too: