ReadCube Release of Papers App

If you’ve read my blog, you know I’m invested in Papers. The majority of my writing workflows use the app.I’ve been following news about the app with trepidation. Papers “teamed up” with RedCube in March of 2016. Readcube / Papers have been working on a new version of the app. Although the screenshots look reminiscent of Papers, there will be at least one major change; Papers is moving to a subscription model. I have not found pricing information yet.The combination of a new version, and unknown pricing model, and a distrust of traditional publishers has left me wanting to explore my options.I’m curious what app each of you is currently using for manuscript management and bibliography generation (and why). Please leave comments below.Addendum: Beware. Updating to Scrivener 3 breaks Magic Citations in Papers. From what I've read online, Readcube is not saying when (or if) this issue will be resolved.

OmniFocus Mail Drop Trick

Here's a quick tip for getting tasks from your email to your OmniFocus Inbox.Many times, requests for my time arrive via email. Committing and tracking this type of request used to be a multi-step process. First, I'd add the email to my OmniFocus Inbox. Then I would reply to the email acknowledging my commitment (or requesting a follow-up).I realized there was an easier way....Now, when replying to an email with a task, I merely put my OmniFocus Mail Drop email address in the bcc field. Using this method, I can respond and track the task in a single button click.

Sense-making of Academic Literature using Tinderbox

I began using a program called Tinderbox many years ago. Although I understood the program was very powerful, I never took the time to dig into its many features. Over the last six months I've been incorporating Tinderbox into my Writing and have been extremely impressed at the depth of features and the incredible capabilities it adds to my workflow.Don’t feel badly if you haven’t heard of Tinderbox—It's a bit hard to explain. One might call it a hypertext personal information management tool—but that description really doesn’t do it justice. If you’re interested and would like to orient yourself to what Tinderbox is, try this Macworld review of Tinderbox 5 (the current version is 7).An increasing amount of my time is now spent thinking about the rapidly evolving information on the human microbiome. I have read hundreds of papers in this domain, but, like most academicians, I struggle to keep track of the things I’ve Taken in, and how it connects to past and future information. I decided microbiome information was the perfect use case for Tinderbox and finally bit the bullet. To say I've been impressed would be an understatement.The first step was getting the abstracts and metadata from Papers into Tinderbox. I used Keyboard Maestro to build a script to automate the process. The script uses TextEdit to build a document that includes the title, authors, abstract, Pubmed link, Papers link, and Papers citation.Once the information is assembled in Textedit, the whole note is copied to Tinderbox.I then put together an assortment of agents that search across the entirety of the imported information and aggregate information similar information under a single heading.The result is the ability to rapidly find related Information, in an organized fashion, on virtually any topic I’ve read. As I digest new information, I add the abstract and metadata to my Tinderbox Inbox and the agents do the rest—duplicating the abstract into the relevent topics throughout my outline.I have been using the collection of abstracts as the starting place for writing manuscripts and grants. Tinderbox can export Individual items, or the entire document outline as OPML—making it easy to import into OmniOutliner, or more commonly for me, Scrivener. I’ve found myself starting with Tinderbox, then making queries in Devonthink as the idea evolves.Although it has taken a significant amount of time inputting the abstracts into Tinderbox, I am already reaping rewards. It worked so well with the microbiome, I’m using the same method (and scripts) with each of the major areas of my academic life: simulation, integrative medicine, and the microbiome.Tinderbox has an incredible feature set, but it has a very steep learning curve. That is where the User Forums come in. There is an active and friendly group of Tinderbox experts more than willing to answer even the most basic question. I have found digging through both the new and old forums incredibly useful while learning to use this incredible piece of software.Although I spend the majority of my time in the outline mode, Tinderbox offers the opportunity to visualize information in a variety of different ways including basic maps, tree maps, and a whole host of other methods. These options add many other possibilities,. There are hundreds of features I have not covered in this entry but will in future entries. The program is so feature-rich, I've only begun to wrap my mind around the many ways Tinderbox can be used.A few caveats with my Keyboard Maestro script:

• The item you wish to extract must be highlighted within Papers
• TextEdit must be running.
• Keyboard Maestro is wonky when it comes to adding carriage returns—when typing the metadata I have to manually place carriage returns to separate information. I deliberately put a two second delay between each paste to give me time to press the return key.
• Do not interrupt the macro-interruption may result in data-overwrite or loss.
• The script gets the reference information from Papers—and prepends a “1. “ before the actual reference. This is both a bug and a feature—because of this, the new reference bubbles up to the top of the information (sorted by title name), but has to be manually removed.

Overall I have been incredibly impressed with Tinderbox and wished I had learned more about it years ago. My investment of time is already paying dividends. I’m currently using Tinderbox to draft a manuscript and a grant proposal. I will continue to blog about features as I learn more about the program. Enjoy.

LiquidText PDF Reader

I have experimented with different PDF readers on my iPad. Over the past several months I’ve exclusively used a program called LiquidText.LiquidText has a unique, award-winning, interface that allows me to drag, drop, and manipulate text using my finger. LiquidText was named “Most Innovative iPad App of the Year” by Apple in 2015. LiquidText feels much more natural than any other PDF reader I’ve used on iOS--and I've used many. After highlighting with my finger, the exerpts / highlights / comments are extracted into their own area. The excerpts may be dragged around, linked, and repositioned at will.When reading and highlighting, I either drag text from the PDF into the notes area, or simply hit “AutoExcerpt” and the text is extracted for me. I can comment on the excerpted information.I can also view the place in the paper the highlight came from by merely touching the excerpt in the notes area.LiquidText reads and writes to a whole range of cloud services, but has limited range of export document choices.An Enterprise version is available for $9.99 that adds features like multi-document search and the ability to comment on multiple documents simultaneously. I've been using the app so much, I upgraded primarily to support the developer.There are a few features that are not (yet) available—the most critical for me is the inability to export highlights into a text file—LiquidText only exports highlights to Microsoft Word. This, unfortunately, is not compatible with my workflow for extracting highlights, but I like Liquidtext so much, I figured out a workaround using Skim—here is my entire workflow:

• I set up a Dropbox LiquidText Folder to serve as a bridge with my desktop.
• I open the entry in Papers on iOS.
• From within Papers I select "open in". -this brings up action menu.



• I open, read, and annotate in Liquidtext. This includes linking the full-text of references to each excerpt (as suggested by reader GH).
• I export the PDF and Notes from Liquidtext to my Dropbox Folder.



• When I get to my Mac, I open the PDF in Skim.
• Under the File Menu in Skim, I choose “Convert Notes” making my highlights into Skim Notes.
• I then process the annotations as discussed in this blog entry.
• (If you want to take the time on your desktop you can also replace the Papers PDF with the LiquidText highlighted version).

Give Liquidtext a try and please let me know what you think.

Drafts Script to Capture Ideas to Ulysses

As I've mentioned in previous writing, I am a big fan of Ulysses. I now do all of my short writing in Ulysses, so I decided to transition my blog idea script from Drafts->Evernote to Drafts->Ulysses.The script prepends "BlogX" and the current date, erases the Drafts file, then places my new idea in my Ulysses Inbox.In Ulysses, I keep three blog related groups: Ideas, In Process, and Published. I no longer have to take time to move my ideas from Evernote to Ulysses. Instead, each idea is submitted to Ulysses, eliminating entirely the need for Evernote. If you use lUlysses, you can adopt this script for capturing other ideas as well. I hope you find it useful.

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.

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:

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:

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:

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.

Programming the workflow

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

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)

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.

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.

My Move to Papers 3 (End of Endnote Redux)

I was a big fan of Papers 2 as my manuscript and citation management software. After reading the early reviews of Papers 3, I was hesitant to upgrade and trepidatious about the future of the software. I went back and took another look at Sente, Mendeley, Endnote, and Zotero. In the end, I decided to stick with Papers.

Fortunately for me, despite the rocky start, the folks at Mekentosj have continued to work on Papers 3. About a month ago, I decided to make the transition from Papers 2 to Papers 3. This was not an easy decision, as changes in Papers 3 have forced me to revise major portions of my writing workflow. Although the transition was painful, I’m convinced what I have now is more robust and flexible than my previous system.

Over the next few weeks, I’ll write about my transition to Papers 3 (both Mac and iOS). I’ll cover the Papers 3 new interface, how I continue to leverage my Papers 2 data (despite the interface and data storage changes), and how I continue to integrate Papers 3 with Devonthink.

I hope you find my experience useful.

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.

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!

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).