My Omnifocus Set-up (Part 1)

I am a huge fan of OmniFocus (OF). I am so dependent on the software, I’m not sure I could function without it. Although there has been much written about the use of OmniFocus, I have yet to see anyone else that uses the software quite the way I do. In this entry, I’ll introduce you to my OmniFocus set-up. In future entires I’ll demonstrate how I use this set-up to maximize the impact of my work in my personal and professional life.My set-up is an amalgamation of many different things I’ve read online. I’m sure, after seeing what I do, others will continue to build on my ideas.The struggle to keep on top of one’s commitments is not new. Before Getting Things Done and OmniFocus, the go to resource for productivity was Stephen Covey’s First Things First (amazon link). This book suggested breaking down your personal and professional lives into various roles (e.g. Researcher, Clinician, Mentor). Each week, within each role, you were to decide up to three important tasks to accomplish (based on both urgency and importance). Each task could be added to one of 4 quadrants:Covey's QuadrantsThe fact that not all urgent tasks are important, nor are all important tasks urgent was a complete revelation for me. Once I understood this, it was much easier to prioritize my personal and professional life. Per Covey, in order to maximize productivity, one is to spend the majority of their time in Quadrant 2 (Not Urgent, Important). Rather than working on projects haphazardly, Covey recommended spending the vast majority of time focused on Quadrant 2 projects. I choose to define Importance as the project’s impact on my long-term goals.I have blended Omnifocus and First Things First (and a little bit of Agile Programming—but that’s an entry for another time) to develop a system that’s truly my own. In the image below, you can see how I organize Omnifocus. I have four high-level folders: Weekly Priorities, Single Tasks, Projects, and Meta.ProjectsMy Weekly Priorities Folder contains three folders: Maintenance, Weekly Priority, and On Deck. The Maintenance Folder contains all the projects to keep my system running—reminders for my daily, weekly, and monthly reviews. The Weekly Priority Folder contains my weekly highest priority level projects (both personal and professional) I chose during my weekly review. The On Deck Folder contains other important projects—if I’m ultra productive and blast through my priority projects, I look in the On Deck Folder for next tasks to accomplish.The Single Tasks High Folder is self-explanatory.The Projects Folder contains two subfolders: Professional and Personal. Within each of these subfolders I have folders that define each of my professional and personal roles. For instance, my Professional Folder contains the following role folders: Administrator, Clinician, Communicator, Consultant, Fundraiser, Innovator/Entrepreneur, Mentor/Teacher, Researcher, Society Member. Each new professional project is placed within the folder of one of my roles.The Meta Folder Contains my Someday/Maybe project folders (things I’m interested in, but have not yet committed to doing). I also store my completed and dropped projects here.After defining a new project, I place the project into one of my personal or professional subfolders. In the Notes Field of OmniFocus, I use Text Expander scripts to label each project by Covey Quadrant. I then may use OmniFocus Perspectives to quickly locate ALL my projects of a particular quadrant.Window_and_PerspectivesUsing these methods, I am able to juggle a huge number of concurrent projects, each week prioritizing those most important to my personal and professional life. In case you’re wondering, I do most of my heavy lifting / organizing on my Mac. I primarily use OF on my iOS device as reference.In a future entry, I’ll explain how I use this set-up in my daily, weekly, monthly, and annual reviews.

Using Hazel to Organize Grant and Manuscript Files

It is almost the beginning of February and thus I am in the throes of writing another grant (2 actually). I thought I'd take a quick break to tell you how I keep my grant information organized using Hazel.I have a folder that has a template for all the subfolders I use during the preparation of the grant. When starting my project I make a copy of this template and name the parent folder including the funding agency, the year, and the type of grant.Folder Template 2Hazel can rename files and subfolders. I take advantage of this feature to keep the names of my files consistent.I navigate to the folder I am working on and set up new Hazel rule to rename the file and subfolders. The rule looks like this:Hazel Script 2Anytime I put a file into a subfolder, it is automatically renamed appending the name of the grant to the end of the file. This appended name is hugely helpful when I go back to search using program such Houdah Spot or Foxtrot.Folder Results 2I use the same method when I'm preparing manuscripts or working on other projects. Using Hazel I never have to think twice-every file I put into the parent folder or subfolder is appended with the name of the project.Try it out.

Retrieval, Annotation, and Capture of Highlights (2016)

I have a unique way of processing scholarly information, I am convinced it gives me an advantage when writing grants and manuscripts--allowing me to find specific notes and related information very quickly and efficiently without having to rely purely on memory. I’ve written a bit about this before, but the process has evolved, so I am dedicating an entry to my updated workflow. The software and utlities integral to this workflow are:

Highlighting in Papers 3Despite lacking the outstanding features of Skim, I am back to reading/highlighting in Papers. I switched back to Papers primarily for synchronization. I do a fair amount of reading on my iPad. Any highlights I make on my Mac become immediately available on iOS. Anyhing I highlight on my iPad shows up on my Mac. Although I prefer Skim, the simplification afforded by doing everything in Papers was irresistable. Here is the manuscript we’ll be working with, highlighted in Papers.highlighting-in-papers-3Export NotesOnce I’m finished highlighting, it's time to process. Within Papers I go to File->Export->Notes and am provided with the following menu box. (1) I usually choose to save the file to my Desktop, as it needs to be easily accessible for processing. (2) I choose "Selected Papers Only" or you I export notes from my whole collection. (3) I choose Plain Text.export-notesFirst Stage of Processing the Untitled Notes File on DesktopHere is the untitled notes file saved to my desktop.first-stage-of-processing-the-untitled-notes-file-on-desktopContents of the unprocessed notes Filecontents-of-the-unprocessed-notes-fileKeyboard Maestro Script to Add Citation + Link and Save FileI have written two Keyboard Maestro scripts to help process my exported notes. The first script adds metadata to the text of the notes file we just exported, then renames the file using the unique Papers Citation. In order to use my script, in Papers, I make sure the correct paper is highlighted. Next, in the Finder, I select the exported note file. I invoke the script and it prepends the unique Papers Citation followed by a Papers Link to the top of the file.keyboard-maestro-script-to-add-citation---link-and-save-fileKeyboard Maestro Script to Add Citation + Link and Save File ContinuedThe script continues on to a save dialogue box where it replaces "Untitled" with the unique Papers Citation. I have to manually remove the curly brackets (as they are disallowed in file naming). I save the file to the Desktop.Download the script here…. You'll have to remove the .txt from the end of the file to use.keyboard-maestro-script-to-add-citation---link-and-save-file-continuedUniquely named Notes File Saved to Desktop.This note I just saved contains ALL of the exported highlights from the manuscript in a single file. As I've talked about in previous entries, I find it more efficient to access a single concept rather than having to dig through an entire papers worth of notes. I developed (along with a few others) a second KM script that copies the Metadata at the top of the note file, parses the single note file into a collection of notes files--one highlight per file, and appends the metadata to each file.Processing highlights in this way has revolutionized my grant and manuscript writing efficiency.Keyboard Maestro Script to Parse Highlights and Append metadata to each notekeyboard-maestro-script-to-parse-highlights-and-append-metadata-to-each-noteDownload the script here…. You'll have to remove the .txt from the end of the file to use.Moving the FolderI highlight the folder on my Desktop, then double click my Shift Key--this invokes a Launchbar action.Screenshot 2015-12-19 16.54.54Launchbar Moves FolderUsing Launchbar I move the text notes to the folder where I keep all the extracted highlights from all the manuscripts I'v read.Screenshot 2016-01-05 11.25.23Ulysses to finish the processAs I've mentioned previously, i use Ulysses extensively in my personal and professional life. I use Ulysses to finish the processing of my highlights, but any text editor will do. (1) Ulysses is pointed to read all the files in my Notes folder--here you see all the individual files extracted from this manuscript. (2) is the text of a single highlight, (3) is the metada added to each file by the KM script. With some notes I will add my own comments, other times, not. (4) are the references that support the statement....these are added manually by reading through the statement and copying each of the corresponding references from the original PDF. I don't go back and forth between the text file and the PDF...instead, I take advantage of Launchbar's Clipboard History.ulysses-to-finish-the-processLaunchbar Clipboard HistoryI merely highlight each reference mentioned, then in bulk I paste each of the references into the note.launchbar-clipboard-historyAppearance of NoteI showed you what this file looked like in Ulysses. Here is its appearance as a free standing text file. Depending on my mood (and time) I may or may not append refernces to each note file.appearance-of-noteCopy PDF to Indexed FolderAfter I've processed everything, the last step is to export a copy of my PDF to a location Devonthink can access.copy-pdf-to-indexed-folderUsing Devonthink to Find Concepts and Related InformationYou may aak yourself why I go to such lengths processing the information I read. The answer is Devonthink. I use the "Artificial Intelligence" of Devonthink quite extensively in my writing. As I mentioned, all the processed highlights, copies of PDFs go into a set of folders on Dropbox. I then Index (not import) the information in these folders (1) so they are "seen" by Devonthink. Why is that important? When I conduct a search (2), I can find the idea I'm looking for (3). By clicking on the "See also" function (4) in Devonthink I can see every piece of related information in my scholarly library (5), including things I have previously written. This ability has revolutionized the way I write.using-devonthink-to-find-concepts-and-related-informationConclusionIn this entry, I have shown you how I read and process scholarly my annotations from manuscripts. Although the process requires an extra ten minutes or so per manuscript, the payoff is immense.Please comment below.

Tripit and Flightview - Automating Itinerary Building and Flight Tracking

I often travel for business. I previously blogged about my love of TripIt-a website with an app that extracts flight and travel information from my email. I merely send my airline, hotel, and car rental confirmations to plans@tripit.com and the site builds a peronalized itinerary. The Pro version has all sorts of other great features, like finding and booking alternative flights.A while ago, I discovered another site called FlightView. Flightview publishes up-to-the minute, detailed information on flights and airport traffic. It works great in tandem with TripIt. And just like TripIT Flightview is able to extract the salient details from an email itinerary, then activate tracking the day you travel.Now whenever I reserve a flight, I kill two birds with one stone by simply forwarding my flight itinerary to both Tripit and Flightview at the same time. I use this simple trick literally every time I reserve a flight.

Using Drafts to journal in Day One

Last entry, I mentioned how I use Drafts to dump information from my brain, then, only after capturing, do I decide where to send what I wrote. I showed you how to save information from Drafts to Evernote. Today, I will  show you how I capture moments in my journaling app, Day One. 

Although I love Day One, I was not entering information often enough. Action URLs are a powerful feature of Drafts. Action URLs-open other applications, then perform functions. In order to increase my capture rate,  I decided to make an Action URL that transfers text  from Drafts to Day One.

Here is how simple it is…..

Drafts Day1 Action.jpg

I have configured  Day One on my Mac and iOS devices to sync. I also enabled the #hashtag feature in Day One. Hashtags are translated into keywords in Day One.

Since enabling this script, I find myself capturing both personal and professional snippets each day. Give it a try!

Embracing Evernote

Workflows evolve. A few years ago I was hesitant to use Evernote because of its proprietary nature. I was using plaintext to capture everything, but had to work out a complex syncing system to be efficient. Over the last year, I’ve overcome my fear and have increasingly built Evernote into my life. I started using it in so many ways, I finally subscribed to thePremium service. I’ve found Evernote to be a flexible and reliable tool readily available on all my devices — both for capture and to find information when I need it.

Here are a few ways I’m using Evernote:

Clipping Service

The first thing I installed when I started using Evernote was the Mac Clipping Tool. Using the clipping tool I easily capture, attach keywords, and annotate pages from the web. Using the “Share” menu in the web clipper, I copy a link to the note directly as a reference in OmniFocus or Calendar entries. When I’m on my iPhone or iPad I use the Action Button (the square with the arrow emerging from the top) to get items into Evernote.

Emailing notes directly into an Evernote NoteBook (premium feature)

I have transitioned my personal email client to Postbox. Postbox, unlike Mail.app, has an Evernote clipping tool embedded into the interface. Sometimes, I’m unable to use either of these methods and will choose to email a note into Evernote. To learn more about this premium feature, read the excellent overview of Evernote email features (including naming the file, placing the file directly into a specific notebook, or tagging the file with a keyword or reminder time).

I most commonly use this method when I’m answering an email, placing my unique Evernote email address and Omnifocus MailDrop Address in the bcc field of my email. Using this method, I can kill 3 birds with one stone (responding to the email, keeping the reference material, making an Omnifocus entry to keep up with the item).

Linking to reference material for Omnifocus or Calendar

Once information is captured Evernote,  each note has its own unique URL. I use this feature extensively to link reference material to OmniFocus and my Calendar. I have different ways of linking depending on the situation.

By control-clicking on a note in Evernote and then selecting “More Sharing” I copy the web-based URL to my clipboard. I then paste the URL into the note field of Omnifocus or into the appropriate field of my Calendar. Then, even when I change devices, I have access to my reference material.

Another method of grabbing URLs is with Launchbar. As I mentioned, I  now use Launchbar extensively. I can select a note in Evernote and then invoke Launchbar, then I select “Evernote – Copy Link of Selected Note.” This copies the URL of the slected note to my clipboard to be pasted into any other app.

Capturing Ideas in Evernote using Drafts

Evernote extends its great power by linking to many other applications. I’ve found capturing snippets of text into Evernote is even easier than the method I described a few years ago using plaintext.

I use Drafts on my iphone and iPad to capture / brain dump just about everything. Drafts is an essential program on my iPhone. Drafts allows me to capture without thinking about what app I need to open. Once the text is captured, Drafts routes the information wherever I choose. I wrote about one way I use Drafts to capture and process meeting notes. 

When I want to capture an idea, I merely open Drafts and type or dictate my idea into the app. When I’m done, I route the information to Evernote using the following custom action:

IMG 0608

The action automatically derives a title from the first line of the text and appends the date and time. Furthermore, it files the note in my “Ideas” Notebook in Evernote and tags the note with the keyword “Ideas."

The note ends up in Evernote looking like this:

Screenshot 2015 11 27 13 29 52

When I get to Evernote, I append further information in the note as needed. I use IdeaX in the header so when I search for a list of my ideas, they are not mixed together with information I’ve gathered from other sources. If I search for a keyword(s), I not only see my ideas, but all the information I’ve gathered in Evernote—very useful.

Capturing Blog Ideas, Lyric Ideas, Quotes, and other Snippets in Evernote using Drafts

I use a similar scripts in Drafts to capture a whole host of other information on the go. Each class of information is filed into it’s own Notebook in Evernote. For example, here is the action I use to capture information for my blog:

 

IMG 0609

 

By incorporating Evernote, I’ve greatly simplified many of my capture processes. I highly recommend giving Evernote Premium a whirl and trying out a few of these workflows on your own. You won’t be disapointed.

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.

Automated Dictation and Task Delegation using Evernote and Workflow App

As usual, David Sparks (Macsparky) inspired me. After finishing the MacSparky Workflow Video Field Guide, I decided to try my chops at buidling something new. As I was exploring the Gallery (the pre-baked workflows that come with the app), one of the examples caught my eye; "Recording to Evernote."I have a twenty minute commute between my home and work. When not listening to audio books, I attempt to be productive. While driving, I'm frustrated by my inability to delegate tasks to my administrative assistant. Before Workflow, in order to send a request (or dictation), I'd have to ask Siri to transcribe an email and then hope for the best. As I'm sure you're aware, Siri makes many mistakes. It's both difficult and unsafe to proof while driving. Siri was not a viable option.That's where Workflow comes in. I built a Workflow that records my voice then, at the same time, sends a link to both my admin and to Omnifocus. Here's how I did it.

Add the "Recording to Evernote" from the Gallery

First, download Workflow. Once you've installed the app, click on the "Recording to Evernote" workflow in the Gallery. Select "Get Workflow." Your workflow will be added to your "My Workflows" Area. Now it’s time to edit.add-the-recording-to-evernote-from-the-gallery.png

Programming the workflow

I didn't change any of the programming at the beginning of the script, but you can.programming-the-workflow.png

Programming the workflow - screen 2

Here is where I altering and appended the built in script:

  • (1) I customized the name of the note and included the current date variable
  • (2) After the audio note is recorded, the file is saved to Evernote. "Get Note Link" retrieves the unique URL for this brand new note.
  • (3) "Copy to Clipboard" passes the URL of the audio to the clipboard.
  • (4) "Send email" command takes the clipboard and pastes it into my email
  • (5) I put my admin's email address is in the "To:" field
  • (6) I included my OmniFocus MailDrop email address in the "Bcc" field (so I can track what I've delegated in Omnifocus).
  • (7) I customized the Subject Field (and appended the current date)

programming-the-workflow-screen-2.png

Add to my Home Screen

Finally, when I was finished programming (and after I customized the color and icon of the button), I added the button to my HomeScreen. Now, when I touch the button a screen comes up that reminds me to "tap to record." I tap, record my message, and then tap again. Workflow automatically saves the recording to Evernote then sends two emails: one to my admin (with a link to the audio recording) and one to my Omnifocus Inbox (where I can keep track of the delegated task).As you can see, Workflow makes automation ridiculously easy. I hope you find this simple application useful.

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.

Cooking up Productivity: Pomodoro Technique and OmniFocus 2

Over the last month I have been experimenting with extending the usefulness of Omnifocus 2 (OF2) on my Mac.  Of all the things I’ve tried, applying the Pomodoro Technique is by far the most effective.

The Pomodoro (Italian for tomato) Technique uses a timer to break down work into intervals. These intervals are traditionally 25 minutes in length, separated by short breaks. Four Pomodoros are followed by a longer break. To get a sense for the technique, watch this short video.

The original description of the Pomodoro Technique used a kitchen timer, but over the last several years Pomodoro Apps have become available. When I dabbled with Pomodoro in the past, my favorite app was Eggsellent. Eggsellent had a clean interface and, more importantly, would auto-populate flagged items from Omnifocus. Unfortunately, since the release of OF2, Eggsellent has been broken, forcing me to look for alternatives. The two applications I’ve spent the most time with are: Vitamin-R2 and Tomatoes.

Neither Vitamin-R2 or Tomatoes are completely right for me. Although both apps have quite a bit of flexibility in timer length and both have visual records of how I’ve spent my time, neither is automated enough for my taste.  Neither app can pull information directly from OmniFocus like Eggsellent could. Vitamin-R2  has limited capabilites to check off completed activities in OF2, but that is the extent of its integration.

Since neither app is just right, the deciding factor for me was aesthetics.  In this realm there is no comparison: Vitamin-R2 is clearly inferior to Tomatoes.

Tomatoes.png

Here’s how the workflow in Tomatoes takes place: I slide an OF2 task into Tomatoes and tell Tomatoes how many Pomodoros the task will take. I click the timer to start and then follow the countdown either in my menu bar or in the app itself. The app records how many Pomodoros have been completed. I’ve been amazed at how competing against a clock solidifies my focus (and helps me to get more stuff done).

That being said, I’d really like an app that is functional, visually pleasing, AND can autopopulate items from OmniFocus 2. The best situation would be for the app to pull a particular perspective out of OF2. If it’s too complicated to pull a whole perspective out of OF2, I would settle for flagged items. Other aspects of the perfect app would be sharing tasks and statistics across computers (and iOS devices) and logging the Pomodoros in my calendar.

Give the Pomodoro Technique a try and let me know how it goes. If you’re a coder and are interested in developing the perfect Pomodoro application, please give me a shout.

Papers 3 Overview

Papers 3 has been re-written from the ground up. There are changes in virtually every facet of the program, from importing to matching manuscripts to storage and synchronization. Before I explain my workflow, I thought it would be important to familiarize you with some of these changes.

You can download a 30 day trial of Papers 3 and follow along with me. Papers 2 and 3 can exist side-by-side without altering your data.

Go ahead and install Papers 3. Once that’s done, let’s take a look at some of the preferences.

Preferences General:

I choose to open (and annotate) my manuscripts in Skim (as I did with Papers 2). For a short time, I experimented with the built in highlighting features of Papers, but they didn’t meet my needs.

Preferences general

Preference: Sync

I want my library to sync across my computers and iOS devices. Here, I’ve turned on Dropbox Sync and checked automatically sync new changes.

 

Preference sync

Preferences: Library

Here are my Library Preference Settings:

  • (1) denotes the location of my Papers Library in Dropbox
  • Hitting the Browse Button (2) places a virtual disk on your desktop that allows access to your entire Papers Library (via paper, author, year, etc)
  • I keep the Copy files to Paper Library folder after import (3) checked
  • I check Organize library folders by subdirectories (4). I use the convention Category Author Year
  • I check Rename Files in Library Folder (5): I use the convention Author Title Source Year

Preferences library

Main Screen

This is the main Papers 3 screen. The terminology I use here is primarily my own–may deviate from what the company calls a specific area.

  • The Library (1) organizes all the media in the program. My Collections includes both manually created folders and Smart Folders (folders created by metadata of the media. Shared Collections allows you to share selected folders with others.
  • The Search Bar (2) allows you limit your searches or change the presentation of your Library
  • The Filter Bar (3) lets you (from left to right) search for a document, view your library, view by Labels, view library by author, view by Type, and view previous database entries.
  • The Viewing Pane (4) is where you view your media. I typically use the “Column” view, but there are other choices as well.
  • Metadata (5) for the paper may be viewed (from left to right) by Overview, Information, Notes, or Activity
  • Metadata Inspector (6) is where you view Metadata and related information
  • PDF and Supplement Window (7) lets you visually see the first page of the actual paper as it exists in the library.
Main screen

Annotations and Highlights in Skim

When I double click on an entry in Papers, the manuscript opens in Skim.

Annotations in skim

Writing Workflow: Have Your Mac Talk to You to Improve Editing

As I’ve mentioned several times before, writing is central to what I do. My research interest in the use of games-based learning and screen-based simulation has me writing constantly, whether grant applications, manuscripts, reports, concept papers, or blog posts.

An annoying fact about my writing: If I stick to visually proof-reading, I inevitably miss something. That’s why having the computer read back to me has become an essential step in my writing.

Having a Mac do this is quite simple—just highlight the text you’d like to hear, and Control-Click the text. Then under the Speech submenu select “Start Speaking.” To stop, Control-Click and under the Speech submenu select “Stop Speaking.”

If you’re like me, you’ll catch omitted words, duplicate words, syntactical errors, and the like. The only downside is if you stop the read-back, you can’t restart from the same spot—you’ll have to start from the beginning.

Because of this, I decided to develop and share two Keyboard Maestro scripts. The first, via a single mouse click, will select the current paragraph (regardless of where your cursor is) and read it back to you. The second, selects the whole document and reads it back. I use the default voice (Alex), but you can change the voice to whatever you’d like from within Keyboard Maestro.

Let me know what you think!

P.S. When you download script to your computer from Dropbox, you’ll have to remove the .txt from the file name.

Updated Keyboard Maestro Script for Obtaining Scholarly Information through Duke

In a previous entry, I published my Keyboard Maestro script that I often use to obtain scholarly literature. A few months ago, Duke’s Medical Center Library updated their website, which broke my script.

I finally had a chance to re-write the script today.

Here is how it works:

  1. Highlight any text (web page, PDF, Word Document, etc.) and hit Command-Shift R
  2. the script will copy the highlighted text
  3. then it will launch Duke’s Medical Center Library Web Page
  4. it will paste the copied text into the search field of the web page
  5. and then submit the search to Pubmed

All this with a single key stroke–saves me tons of time.

If you’re not a Duke, you will have to modify the URL and search boxes to conform to your library of choice.

Don’t have Keyboard Maestro? Get a demo!

Enjoy.

Addendum, May 17, 2014:  Several folks reported the script didn’t work for them. I’ve modified the script again. You can download the updated script here, and import it into Keyboard Maestro. When you download the macro and before you import, you’ll have to remove the .txt at the end of the file (so it will be recognized as a Keyboard Maestro file).

Writing and Reading Workflow: Batching and Automating Full-Text Retrieval

In my work at Duke University on simulation, games-based learning, and learning technology, I frequently read and write scientific information. I’ve developed a series of workflows to help me efficiently deal with information when writing papers and grants. In a previous entry I talked about how I try to batch operations, doing similar things at the same time. This entry will be about my workflow for reading scientific manuscripts.

I use Skim for scientific reading, typically using the bottom pane of the “Split PDF” feature to look at the title of references as I come across them in the body of the manuscript. On average, I’m interested in downloading about 10% of these references to my personal library.

Although I love Skim, one feature I have not been able to figure out is how to highlight items in the bottom split screen. Thus, I’ve created a workaround. Before I start reading an article in Skim, I create a note called “Get Manuscripts” As I’m reading, I merely record the references number of articles I want to fetch in my “Get References” note. Because I create this note first it’s always located at the top of my Skim Notes. When I’m done reading the current article and processing my annotations, I retrieve the supporting articles I identified while reading. 

To do this, I use a phenomenal program called KeyBoard Maestro. Keyboard Maestro lets me type a single keyboard command to trigger an entire workflow. One by one, I work through my “Get References” numbers, highlighting the title of each corresponding article. After highlighting each title, Keyboard Maestro does the rest (invoked by Command-Option-R).

Keyboard Maestro automatically  (1) copies my highlighted text, (2) surfs to the Duke Library literature search page, (3) pastes the text string into the appropriate field, and (4) submits the search. Thus, with a single key combination, I am able to download the full text of supporting literature. Once I find the full text I'm interested in (usually a PDF), I save it to my Download Folder, where Hazel takes over and imports the paper into my Papers Library.

If I'm not ready to retrieve the articles, I create an Omnifocus Action for each to be collected at a later time.

My macro is not limited to Skim, it works with any text I’ve highlighted, be it on the web, in a manuscript, or somewhere else. Here is a picture of the programming, but obviously, you’ll have to modify it for your own favorite full-text repository. Enjoy!

Maestro Automate Full Text Retrieval

 

Addendum (January 14, 2014): If you’re searching at Duke, you’ve probably noticed the library changed its search interface. I’ve updated the Keyboard Maestro Script accordingly. It’s only configured to search for peer-reviewed articles. Download the script and import it into Keyboard Maestro (will only work for Duke Libraries).