Writing with my Voice

In my academic roles in the Duke University Human Simulation and Patient Safety Center I write a great deal. I write manuscripts, grants,white papers, and a whole host of other material. I’ve read the most efficient way to write a long document is to spew everything into a draft as quickly as possible, then go back and edit.Typing slows me down. The fastest way for me to “write” something is with my voice. I find it easier to adhere to this ‘draft first’ rule when I dictate using my voice rather than typing out a draft on my keyboard.Why is this? When I type, I tend to correct errors as they occur. Even worse, I try to polish each sentence on the fly (rather than powering through the entire document at one time). The constant editing interrupts my thoughts and makes slogging through an whole first draft extremely tedious.Lately, I've been using a workflow that takes advantage of the native iPhone’s dictation feature to “write.” This workflows has sped up my writing significantly by forcing me to keep moving forward while allowing me to write anywhere/anytime.This workflow is relatively easy to set up. Here is the software you’ll need.OmniOutlinerOmniOutliner is, you guessed it, an outlining program. Before I write anything, I use OmniOutliner on both on my iPad and on my Mac to plan my document. The Omni Group recently added the ability to sync to iCloud (currently a beta feature). Universal access to my outlines allows me to draft and rearrange my outline on the fly, regardless of location.ScrivenerThe next piece of software is Scrivener for Mac. Scrivener is an essential writing programs. That’s right, essential! If you don’t use Scrivener yet, stop reading and download the software right now.One of the advantages of Scrivener on Mac is it allows me to write in chunks. I can start writing in the middle of my project. When I sync the Scrivener project to Dropbox, I end up with a number of text files (each representing one ‘chunk’ of the Scrivener Project). Being able to write non-linearly from anywhere allows me to complete a draft very quickly. I am able to knock out sections of a document while in my car, walking between meetings, or anywhere else the urge to write hits me.Chunks of text in Scrivener may be moved around ad nauseum. I take advantage of the ability to move things around quite frequently. If I don’t like what I’ve changed, Scrivener has built in version control , so I can revert back to past drafts.Scrivener exports pieces of the project as individual files. Scrivener puts all these files in a “Drafts” folder inside the folder of your choice. These files can be txt, rtf, or other formats. I use text since I write in Markdown.DropBoxI set up a folder in my DropBox hierarchy called “Writing Sync.” It is here I synchronize my project between Scrivener and Editorial. Each new project gets its own folder.EditorialEditorial is a phenomenal text editor for iOS with a slew of built in features. Editorial allows me to edit documents written in Markdown and has a wholebunch of other features that makes it my go-to document editing software on iOS. Editorial, unsurprisingly, syncs with DropBox. I have Editorial point to my  “Writing Sync” in Dropbox.Now that I’ve discussed the software I use, let’s set everything up.The WorkflowThe first thing I do is draft my outline in OmniOutliner. I typically do this on my iPad or my Mac then rearrange the outline until I'm happy. Once my outline is complete I export it as an OPML file.I create a blank Scrivener project, then import the OPML file into Scrivener. Importing the OPML populates the Scrivener project, preserving the hierarchy of the outline. Each bullet of the outline receives its own individual chunk in Scrivener.The next step is to set up synchronization of the Scrivener with Dropbox. Under the File Menu, I go to Sync->With External Folder….I make sure the back up before export box is checked and make sure that the project is exported as text. I select the “Writing Sync” Folder as the text file destination. I hit okay and the entire Scrivener project is exported to "Writing Sync" as individual text documents (Scrivener assigns a number to the front of each text file to keep them in order).On my iPad or iPhone, I point Editorial to my “Writing Sync” Folder. Within Editorial I can edit each of the individual text files. I open the file I wish to write/edit and use the dictation (Siri must be enabled) on My iPhone. Editorial immediately synchronizes the new text back  into Dropbox.Once I return to my Mac I re-synchronize the project in Scrivener. All the files in Scrivener now reflect my writing from Editorial. One I've completed my first draft, I use this same back and forth method to edit.Once I'm happy with each of the chunks, I go back to Scrivener on my Mac and compile the whole document as a single Markdown file. I save this file a level above the “Drafts” Folder Scrivener created when syncing.I  can access the full document using Editorial (or any other text editor) on my Mac or iOS device (I use Byword or Ulysses on my Mac) . Finally, when I'm done polishing, I export the document to Microsoft Word (or to the web). Using this workflow, I can write something in about 1/10 the time it used to take me with a keyboard. Although this method works well, it is not without a few annoyances. iPhones limit dictation to 30 second chunks. In addition, Editorial tends to chop off the last few words of a sentence after those 30 seconds expire. Because I’m working on segments of the overall project and can dictate quite a bit in 30 seconds, this is not a huge deal for me. When drafting, the key is to keep pressing forward.This workflow has literally changed to way I write. The workflow allows me great deal of flexibility and saves me a great deal of time.

Taekman Writing Workflow 2015

The early release of Papers 3 got a bad rap, and rightly so. My negative experience began as I imported my Papers 2 library into Papers 3. I had about 2500 papers, but only a fraction of these PDFs were imported properly. I am still recovering from these import problems--having to add each missing PDF by hand. Although importing was a issue early on, The makers of Papers, MekentosJ, now part of Springer Science+Business Media, worked hard to fix problems. I assume, with all the work on Papers, that importing has been fixed. My advice? Back-up your data before trying to import to Papers 3!

Although I had early problems, I can tell you that Papers 3 is pretty robust now. I recently used it to write and submit a full grant. I’ll say the app should be strongly considered if you’re looking for a reference manager / bibliography builder. If you’re interested in some of the changes in Papers 3, check out this entry.

With the release of Papers 3, all files and PDFs are bundled into a single container. Bundling makes syncing across computers more reliable, but indexing of individual files much more difficult. Unfortunatly, my Papers 2 workflow was dependent on indexing of single files. And thus, with the release of Papers 3, I had to revamp my writing workflow. That’s what I’m going to cover in this entry.

My current workflow has three parts: 1.organizing, 2. creating, and 3. writing/formatting

The software I use includes:
Papers3
DropBox
Hazel
Skim
Keyboard Maestro
Ulysses
Devonthink
Tinderbox
OmniOutliner
Scrivener
Pages or Word

Part 1: Organizing

Papers 3

Papers is used as my storehouse for all academic literature. I use Keywords and Smart Folders (akin to Smart Playlists in iTunes) to keep my literature sorted. In addition to the topic of each manuscript or book chapter, I use keywords such as "MustRead" that fuel my prioritized reading list. I tend to keep my library sorted by the date in the main window, but can easily search or sort my library in numerous other ways. My library is synchronized using Dropbox.

KeyBoard Maestro

Most people, while reading academic literature, find additional manuscripts they’d like to download. I’ve developed a series of KeyBoard Maestro scripts that simplify the download of these additional articles from Duke’s Library, Pubmed, and Google Scholar. As I’m reading a manuscript, I highlight the article I want to download and invoke my KM script. The macro copies the text string I’ve highlighted, goes to the appropriate web page (e.g. Duke’s Library), pastes the search string into the appropriate box, and hits submit. Thus with two keystrokes, I can find and download new PDFs I’d like to read. The new PDFs are sent to my “Downloads” folder. Then Hazel takes over.

Hazel

Hazel is a program that watches folders on my computer. When a file matches defined criteria, Hazel performs a script. I have a Hazel script watch for PDFs that contain the word “Reference.” When Hazel sees a file that matches, it launches Papers and imports the file into my library.

Skim

Despite the pleasing new main interface, Papers 3 highlighting leaves much to be desired. For reading and annotating scientific literature I use Skim (Skim can designated as the primary PDF reader in the Papers Prefernce menu). Skim has a robust feature set and is customized for academic literature. Oh, and it’s free! When I’m done reading and annotating, I export the Skim annotations to a PlainText file. I then use a KM script to name the the Skim Notes file to my convention.

Using another KM script, I parse the single notes file into separate text files (one for each highlight or annotation). Each file is named to convention and contains the text I highlighted in the manuscript, my own comments, and the full reference. All the individual notes are aggragated into a folder. I move this folder from my Desktop to the cloud so I can access it from anywhere. I call this my Literature Comments Folder. Now I move to Ulysses.

Ulysses

Ulysses is able to read files anywhere on my computer. I’ve configured Ulysses to point to my Literature Comments Folder so all my comments are available in an organized fashion. At this point I can add additional comments to my individual highlight files. The next step is to index the files in Devonthink.

Devonthink

Finally, I open Devonthink. This workflow has matured from what I discussed in this entry. I have a database that is solely used to index my scholarly reading. From the File Menu, I update the index (NOT import) of my Literature Comments Folder. Indexing this folder allows me to take advantage of the “Artificial Intelligence” of Devonthink, finding relevant information throughout my reading.

Part 2: Creating

Tinderbox

At this point I’m ready to start developing my scholarly work. I use Tinderbox (in Outline View) to generate a high-level preliminary outline. Tinderbox is a power-user’s application. I’ve only scratched the surface of its capabilities, but find it extremely useful early on to organize thoughts and find connections between what I’ve read and what I hope to write.

From within Devonthink, I review each of my comments. If I find something I want to include, I drag and drop the file (comment, reference, and highlighted text) into Tinderbox. Then, using Devonthink’s “See Also & Classify” command, I see related notes in my Literature Comments Folder . I drag and drop the additional comments into Tinderbox too. As I think of new ideas, it’s not uncommon for me to conduct a freeform search from within Devonthink to see which comments bubble to the top.

Once I have several dozen comments in Tinderbox, I find myself entertaining new thoughts, and often adjusting (or add to) my outline.

Another way I approach the creative process is to surf through interesting comments and move them one by one into Tinderbox without organizing them (usually in the Map View). Once I have a few dozen of these interesting quotes and highlights, I start to see connections between them, letting me further refine and organize my thoughts (and begin to develop and outline).

Once I’m satisfied with my outline, I’ll sometimes export to OmniOutliner for additional organization. But most times, I’ll export my outline directly from Tinderbox to Scrivener.

Part 3: Writing and Formatting

Scrivener

Scrivener is the place where the early versions of my manuscript are built. Scrivener imports OPML files from Tinderbox or OmniOutliner—each bullet of the outline gets its own content field. I do the majority of my early writing in Scrivener, attacking whatever section I feel like writing at the time. I use the Magic Citations of Papers 3 to insert my references as I write. Once I get words down on the screen, I often find myself tweaking the outline in Scrivener. This early phase, when I’m writing on the go, is when I yearn for the iPad version of Scrivener. Until that’s available, I’ll continue to use Scrivener’s synchronization with SimpleNote when I plan to write on my iPad.

When I’ve completed all the sections in my Scrivener outline, I’ll export everything I’ve written to Ulysses. I use Ulysses to edit and rewrite (in Markdown) until I think the work is ready for submission. As I’m importing and editing my paper in Ulysses, I make sure to have the document type set to Markdown (not MarkdownXL). MarkdownXL uses the curly brackets as an internal mark for annotations. If I use MarkdownXL in Ulysses, all of my Papers citations are formatted as footnotes—very annoying.

Word or Pages

I write and edit for several rounds in Ulysses. Ulysses for iPad makes this process more seamless and enjoyable. Unfortunately, when I’m done writing, I cannot format my bibliography in Ulysses. I have to export my file to Word or Pages. That’s okay though, I still have to format my paper. I use an old version of Pages (the new version of Pages still doesn’t allow bibliography formatting). Microsoft Word also works. To do this, I highlight all my text and from the Ulysses Edit Menu I select Copy as RTF (Word), then paste it in the word processing application. After my bibliography is formatted, I format the rest of the paper.

Finally, as the final check of my writing, I use a KM script to read back the text to me. I often find errors, even in this late phase of writing. Finally, I double check everything conforms to required format of the journal (or funding agency) and hit submit.

And there you have it: my writing workflow. As with most of my workflows it is continuously subject to improvement. For the time being this workflow has streamlined my writing. I hope it works for you too.