One of the most popular entries on WIPPP has been my 2015 Writing Workflow. My workflow has changed substantially over the last several years. I thought I'd share what I'm currently doing.

Some criticize my workflow for its complexity, but I can assure you that it is amazingly functional once set up. I can't imagine working any other way.

I'll start with the "meta" infrastructure programs that make the whole workflow run, including the set-up. I'll then cover how I collect information. After that, I'll write about how I read and synthesize the information to help with sense-making. Then, I'll go over extracting information. Finally, I'll take you through the writing process, from concept to manuscript/grant submission. I've included links to past articles to show how I've set up my infrastructure.

Software

Infrastructure

• LaunchBar 6 - Used for many functions including extracting and searching for references found in manuscripts, saving annotations, launching apps, etc.

• Hazel - Runs in the background on my Mac to automatically add PDF manuscripts to Bookends.

• Dropbox - the location of my Scrivener and Devonthink files.

Collecting and Extracting

• Drafts - Used for capturing ideas and anything else that comes to mind (see this entry, and this one)

• Read by QxMD - "Flipboard for scholarly information." How I'm finding the majority of new literature lately (blog entry-Keeping Current with Bookends and QxMD Read)

• OmniFocus - Where I store the manuscripts I can't immediately retrieve—for batch retrieval at a later time.

• Highlights - to extract annotations from all my scholarly information.

• Bookends -powerful bibliographic management for my Mac. I also use Bookends on iOS.

Synthesizing

• Devonthink 3 - to follow RSS feeds of journals, for research and capture my annotations and also to search through annotations.

• DEVONthink To Go - used to search for information on the go.

• The Archive - for Zettelkasten management (What the heck is Zettelkasten?)

Writing

• Scapple - used for brainstorming

• OmniOutliner - Used to outline manuscripts and ultimately to export outline to Scrivener in OPML format

• Ulysses and Bear - for short document writing (e.g. blog entries and creative writing).

• Scrivener - my workhorse for long writing (grants and manuscripts). I honestly could not do the academic side of my job without this software.

Set-up

Hazel recognizes any manuscripts saved to my Downloads Folder. Once matched, Hazel sends the file to Bookends.

Hazel monitors folders on my computer and acts on individual files according to rules I create. Hazel can even peek at the content of files and "recognize" what's inside. I have Hazel monitoring about a dozen folders on my Mac, but my Downloads Folder keeps Hazel the busiest. I have about two dozen rules running on my Downloads Folder alone. For this particular writing workflow, I ask Hazel to look at the contents of every PDF in my Downloads Folder and match files that have words unique to scholarly publications. I've found matching the matching criteria works the best. (I now use DOI instead of the term References, avoiding the import of annoying things, like CVs, into my Bookends database).

Bookends syncs via iCloud (Mac and iOS).

Devonthink indexes (not imports) multiple folders including:

1. the PDF folder generated by Bookends in iCloud,
2. The Archive Folder in Dropbox, and
3. my Annotations Folder in Dropbox.

My Devonthink database is synchronized via Dropbox to Devonthink To Go.

Collecting information

I collect information using QxMD Read, Twitter, or Devonthink RSS to find new literature. Less commonly, I conduct formal searches in PubMed or Google Scholar on the web or through Bookends. Other times I use Launchbar or Highlights to download literature I've found in the Bibliography of a manuscript.

Once I've found the information I'd like to read, I attempt to download the PDF. In iOS, If the PDF is available, I open the PDF with Bookends. Opening the PDF in Bookends imports the reference and PDF into the Bookend database and grabs the metadata.

If I'm on my Mac, I download the paper to my Downloads Folder. A Hazel script automatically launches Bookends and imports the manuscript into Bookends.

If the PDF isn't immediately available—I capture the reference to OmniFocus until I'm at work or when I sign on to work's VPN.

Reading and Synthesizing

I read manuscripts almost exclusively in the Highlights app on my Mac or iPad. As I'm going, I highlight and make comments on the annotations. I read the entire paper through to the end, highlighting and commenting as I go. If I want to retain a significant point of an article, I make a Zettel (using my Zettel Template in The Archive on my Mac, or Drafts on iOS).

Extracting information

My extraction process has changed significantly since 2015. I highlight the manuscript using Highlights App (either on my Mac or my iPad). After I annotate the paper, I'm ready to process it to make the information accessible to my writing system. I make sure my Bookends Library is synchronized and then work from my Mac.

I no longer extract my annotations as individual files (this was far too labor-intensive and messed with the accuracy of Devonthink's AI). Instead, when I'm at my Mac, I open the paper from Bookends using Highlights. I make sure the metadata has been captured in Highlights (this ensures the proper information link back to Bookends). Then, I export all my annotations and comments as a single HTML file saved to an Annotations Folder in Dropbox. Finally, I index (not import) the Annotations Folder on Dropbox into Devonthink. This new workflow works much more reliably with Devonthink's AI.

Why HTML? Honestly, I'd prefer to use the Textbundle format, but Devonthink To Go is not able to recognize Textbundles. I like HTML documents because they include figures. Later, if I want, I can convert the extracted annotations into a PDF, but thus far, the Webarchive HTML files work well.

My Devonthink Writing Database has multiple indexed folders, including The Archive, PDFs from Bookends, and my extracted HTML Annotations. I have my RSS feeds of scientific literature in a separate database. Devonthink's AI finds recently published papers related to documents in my library.

Putting it all together

Blog and Short Document Writing - Ulysses and Bear

For creative writing, I now use Bear. I love Bear's writing environment (I think it improves my creativity) and use it for personal stories and songwriting. Blog entries, I write in Ulysses. Ulysses and Bear's multi-platform support and seamless synchronization are priceless for writing. Because I'm a bit fearful of proprietary formats, I am diligent about backing up my work. I use an Omnifocus reminder to backup both my Bear and in Ulysses database every week.

Manuscripts, Grants, and Books - Scrivener

For longer writing projects, nothing compares to Scrivener. Scrivener is a complete writing studio. I use the software regularly. I often use Scapple (created by the same developers as Scrivener) to plan the manuscript at a high level. To build my Scapple outline, I brainstorm ideas (including many trips to Devonthink). I prefer Scapple over other mind mapping software as it is less constrained on parent-children relationships.

Although I capture information differently from 2015, my use of Devonthink for finding information remains relatively unchanged. See the following entries:

• Automating The Organization And Accessibility Of Academic Literature: Bookends And Devonthink Pro
• Unlock The Power Of RSS Feeds With Devonthink

I can brainstorm and then move ideas around. I no longer use Tinderbox. Although very powerful, I spent far too much time trying to master simple tasks in Tinderbox rather than getting work done. Maybe I'll pick it up again in the future.

Once I've outlined my paper in Scapple, I export the Scapple file to OPML. If the outline is ready to start writing, I import the OPML file directly into Scrivener. If I want to tweak the outline more or add additional information, I open the OPML document in OmniOutliner.

Once my outline is in Scrivener, I start writing. The modern version of Scrivener synchronizes between all my devices, Mac and iOS. When I need to find a concept or citation, I turn to Devonthink either on my Mac (usually) or iOS (in a pinch). When I find something I want to use in my writing, I click the link at the top of the page on the HTML document.

Clicking the link takes me to the corresponding reference in Bookends. I find the text from the annotations in the Bookends and copy the note (or notes) by right-clicking.

I then paste the note under the appropriate heading in Scrivener (or in Scapple or OmniOutliner if I'm still organizing). The single annotation is copied from Bookends along with the coded citation that will help Bookends compile my Bibliography.

Once I've pasted the note in Scrivener, I change the text color to blue. That way, I know what words I copied verbatim. I use Scrivener to track the state of various parts of the project. I use the interplay of Scrivener and Bookends to cite references as I'm writing. Different sections of my project go through multiple drafts—Scrivener tracks the phase of each component.

When the project is nearing completion, I export the project to Microsoft Word. There, I put the final touches on the manuscript. I then use the Speech function of my Mac to read each paragraph of the document back to me. I'm always amazed at how many errors I catch in this last phase of writing. Finally, I format the paper and Bibliography with Bookends. At this point, the information is ready to submit.

This is an overview of my current writing workflow. I’m curious to see what others are doing and/or how you riff/build on my workflow.

Until next time……