Improving my research and writing workflow

Screenshot of Zotero for Mac
Zotero for Mac

This year I realized that what I tell students, “If the writing is hard, you have not done enough reporting,” is true also for academic papers and projects. Having to find / read / understand / synthesize dozens of research papers and book chapters is not a skill I had to formally develop when I was in school. But recently, several short and long-term writing projects have shown the folly of having no process. I needed to read more, but also manage the information better.

So to further procrastinate on actually writing, I spent a couple of weeks on-and-off improving my workspace. Details below. FWIW, I have a Mac and some of the apps are Mac-only. There might be PC-alternatives but I have not looked into those.

After test-driving EndNote and Mendeley a few years ago, I settled on Zotero as a reference manager. It is free, open-source and has a decent development community. That is important as the user-developed plug-ins are key. It does not yet have an iOS app, though PaperShip still more or less works.

Some of these tools require a familiarity with Python and tools like HomeBrew for installing and managing software packages like PyZotero. Each app includes documentation and walk-throughs that you can learn from if you take it slow. A full list of apps, tools and links is at the bottom.

Finding, reading, annotating, archiving

Find it!

At Mizzou this means Google Scholar is proxied and search results are either one-click away from the article PDF or a “Find it at MU” link is inserted onto the page.

My workflow is: Use Google Scholar to find relevant journal articles, one-click download them into Zotero, OCR if necessary and then highlight and leave notes in the PDF as I read. I then go to the collection of references I am working with and select “extract annotations” which creates an attached RTF file with every highlighted word and note. This alone is a huge time saver. You can just ignore the rest of my list here and happily get the above tools up-and-running in fifteen minutes.

Information management

Having easy access to the annotations is great, but they are still isolated across 20–30 files in a Zotero collection. For convenience, I really want to gather all of the Product Management notes (for example) into one file for reference.

Snippet from Zotero Workflows on GitHub

The workflows are all fairly simple Python scripts but they combine the highlights and notes from dozens of PDF files into one text document making it much easier to find and use a reference I read a month ago. The RTF file also includes an anchor link back to the original PDF so it is an easy index of what I have read on a given topic.


I have done three things with Alfred:

Keyword and query for Zotero Collections to extract notes using an Alfred workflow.
Keyword and query for Zotero Collections to extract notes using an Alfred workflow.

Finally, not at all required in the process, but I also use DevonThink as a local archive and search engine for everything that does not go into Zotero. So all of the extracted notes files are indexed by DevonThink and also made available on my mobile devices for easy access.

For actual writing, I am using Scrivener. Notice how that comes last on the list. There are some interesting possibilities there to further integrate Zotero’s citations during writing and output but I have not yet gotten that far.

List of ingredients



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Damon Kiesow

Knight Chair in Digital Editing and Producing @mujschool. Formerly Director of Product @McClatchy Also: @BostonGlobe, @Poynter, @AOL, M.S. HFID @bentleyu