Keeping Current with Bookends and QxMD Read

In a previous entry, I covered the ways I add new literature to my scholarly manuscript collection. Technology has evolved since that entry. I’ve migrated to Bookends to keep my literature organized, and I have additional ways I find new literature I’d like to read. That’s what I’d like to cover today.In my MacWorld entry (circa 2012), I mentioned the three ways I collected new reading material:

• as a recipient of an Endnote library (when writing collaboratively)

• through personal searches on the web (and liberal use of Google’s automated search terms)

• as attachments to colleague’s emails

Since then, there are two methods I use even more commonly:

• Following individuals with similar interests and using keywords in Twitter.

• Using QxMD Read

Until recently, I was not familiar with QxMD Read. A colleague at Duke, Dr. Jordan Komisarow, brought the app to my attention. According to QxMD, Read “provides a single place to keep up with new medical & scientific research, read outstanding topic reviews and search PubMed. This iPhone & iPad app provides a simple interface that drives discovery and seamless access to the medical literature by reformatting it into a personalized digital journal.” One comment describes the app as “The Flipboard of Medical Literature.”The app was easy to set up. First I made a QxMD username and password. Then I chose my professions of interest. Finally, I chose specific journals, keywords, and collated collections.Once set up, Read began scouring the medical literature for new articles.In a single screen, I scroll through all the new publications (titles, conclusion, journal, etc.).If I find something of interest, I click on the title to find more information, including the entire abstract. While I’m scanning the abstract, Read attempts to download the full-text PDF.About half the time, Read finds a PDF and downloads it into the app. If the PDF cannot be found, I email the entry to my personalized Omnifocus Mail Drop so the paper is added to my Omnifocus Inbox.If the PDF is downloaded into Read, it is then a simple task to move the document into Bookends. The ease of importing full entries is one of the many places Bookends outshines Papers. I click Open In… and then select the Bookends icon.Bookends works its magic, finding one (or sometimes more) suggestions as matches.I choose the matching metadata and Bookends imports the PDF and metadata into its database. The paper and its metadata are immediately available on all of my devices.The process works pretty seamlessly. The only annoyance is that if you save the PDF to your library, it receives a numerical name. You must later open Bookends on your Mac and rename the PDF to your naming convention. This is a small price to pay for such power.I'm finding even more relevant information these days using QxMD Read. My challenge now is finding the time to read and process it all!

My Migration from Papers to Bookends

I have dedicated a lot of time and energy squeaking every ounce of productivity from the Papers app. I’ve used Papers for more than a decade. Over the years, I built many scripts and work-arounds to address the shortcomings of the application.ReadCube purchased Papers in 2016. Because of the time I’ve spent in Papers, I started having angst when I read of certain changes to the software: a subscription model, the loss of Magic Citations, and the loss of integration with Scrivener.I started exploring alternatives to Papers. When I wrote about my interest in migrating away from Papers, several Wippp Readers suggested I check out Bookends. Several folks raved about the tight integration between Bookends and Devonthink as well as Bookends and Tinderbox—two other programs I use heavily in my academic life. Several people also mentioned the LEGENDARY support of SonnySoft, the company  behind Bookends.My initial evaluation of Bookends was far too cursory. Following publication of the blog entry, I received a very nice email from SonnySoft asking me to take a closer look at Bookends. After digging deep into the software, I decided to migrate from Papers to Bookends. I haven’t looked back. It’s been several months now and the more I use Bookends, the more I like it.Things I like about Bookends:

• The interface, although not as modern as Papers, is cleaner and more organized.

• The iOS and Desktop version are better integrated than Papers.

• A PDF on my phone is drop-dead easy to import into Bookends. The PDF and the metadata I choose is automatically synced with the Mac app (although I have to rename the pdf when I get to my Mac).

• All PDFs are saved to a single folder in iCloud, making them easy to access and for Devonthink to index.

• Bookends integrates well with Scrivener (and many other writing clients)

• Dragging and dropping citations into Tinderbox and Devonthink are both seamless. Tinderbox maintains metadata from Bookends. This obviates the need for the KM script I built to move citations from Papers to Tinderbox.

Things I don’t like:

• It was difficult to import Papers library with PDF into Bookends (Bookends only imported about 1/3 of my PDFs).

• I can't export or customize the format of the exported metadata.

• My smart collections don’t transfer to iOS.

• Although I can designate a “watch” folder to import new PDFs into Bookends, this only works with PDFs that are saved to the folder AFTER Bookends is open. This didn't work well with how I collect information so I decided to modify my Hazel script, changing it to launch Bookends instead of Papers.

• I don't like the way duplicate references and / or PDFs are handled.

Over the next few months, I plan to write several entries about my migration and how Bookends has become a critical part of my augmented writing workflow.

Papers 3 now supports Scrivener 3!

I had a pleasant surprise today. I opened up Papers to find an update. The update includes support of Magic Citations in Scrivener 3. Thank you ReadCube!

Deliveries Automation - The easiest way to track your packages

Here is a quick tip I wish I figured out before the holidays….There is a nifty application for Mac and iOS called Deliveries (by JuneCloud). The app aggregates tracking information of all your packages. I used it over the holidays to track the progress of my gifts. Out of the box, the app uses iCloud to sync data between your iPhone, iPad, and Mac. Although Deliveries has handy features, it was a multi-step process to get my tracking numbers into the app.The app was so useful, I decided to figure out a way to automate the process of tracking number extraction. JuneCloud was way ahead of me. It turns out there are two ways to sync data in Deliveries: through iCloud or through JuneCloud’s own cloud service, JuneCloud Sync. If you sign up for a JuneCloud Sync account, you can send an email with a tracking number to track@junecloud.com and Deliveries takes care of the rest.I find auto-extraction from forwarded emails extremely easy to use and is a key feature of several of my favorite apps (e.g. Tripit for travel itineraries, of FlightView for flight tracking).I wrote a rule for my email client, Airmail, that automatically forwards tracking emails to the JuneCloud Sync Service:Although I’ve only been using JuneCloud Sync a few days, so far it’s worked flawlessly (with Amazon packages) and has saved me the hassle of cutting and pasting tracking numbers from emails. I’ll report back if I have any trouble with other vendors.

Folder Structure to Maximize Writing with Devonthink Pro

On several occasions I have written about how I use Devonthink Pro (DTP) for scholarly writing. Although at one point I had all my information on manuscripts in a single DTP database, over the last year I have maintained separate databases; one for PDFs, another for my annotations.I accomplish this by having separate folders in Dropbox. After extracting my annotations from Highlights.app, I place the exported files in their own folder. Once a month, I export all the PDFs in my Paper’s Library to their own Dropbox folder. I use a Hazel script to throw away any duplicate PDFs in the Dropbox folder. I index (not import) the annotations folder into one DTP database, and index my PDFs into another.This setup allows a fair amount of flexibility. Not only is this setup advantageous for writing with DTP (as I will cover in my next entry), it allows easy access to my PDFs for reading with Liquidtext or listening with Voice Dream.

Highlighting PDFs from Within Scrivener

Here is a quick trick to use with Scrivener.I’ve been working on some short executive summaries. For longer projects I tend to keep my research in Devonthink. For these shorter reports, I’ve been importing all the supporting information into Scrivener. On several occasions, I’ve wanted to highlight PDFs within Scrivener.It’s very easy to do. In Scrivener, just click on the button indicated in the picture to launch the imported PDF in your default reader.Holding the button down lets you select a different PDF Reader (and lets you choose to make it your default application). Any highlighting changes are saved back to the PDF in Scrivener. I've used this trick numerous times over the past few weeks. I hope you find it useful too.

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.

Highlights.app Redux

I was too quick to judge the program Highlights. I gave Highlights a second chance, and although not perfect, the app is slowly winning me over. Highlights has greatly sped up the extraction of information from my reading.First a little background. I use Papers for my PDF and bibliographic management. I’ve written about how I extract highlights and annotations into individual files along with their relevant references. The reason to go to this trouble is to enable Devonthink’s artificial intelligence. The Devonthink AI uses word count to find related information in other files. I use this method extensively in my writing of grants and manuscripts. With my previous method, I found by adding references to each annotation (thus similar words) I was interfering with Devonthink’s ability to find relevant information. In order to improve Devonthink’s accuracy, I stopped adding references to each individual annotation. Instead, I merely include a Papers Link back to the original file.Highlights shows the annotations you make in the app's right-hand column. A pop-up interface within Highlights allows you to make comments, underline , change colors, etc. The killer feature of Highlights is single-command extraction of each annotation / comment to its own file. This feature allows me to extract highlights (and metadata) without having to invoke my Keyboard Maestro macros. When the data is extracted into Devonthink, the individual files are in Markdown. This makes the extracted information easy to view and edit.Although I’m more enthusiastic about Highlights, there are several quirks you should understand:

1. When Highlights explodes your annotations into individual files, it prepends the original file’s name. If you use Highlights from within Papers (e.g. selecting Highlights as your PDF reader of choice from within Papers) you will end up with a ridiculous, machine based title in your metadata. This is not Highlights fault. The use of non-intuitive file names is one of my pet peeves about Papers. The workaround is to export a copy of the PDF to your Desktop and then launch the exported file using Highlights. Using this method, the author’s name and the title of the manuscript along with the year of publication are all prepended to each markdown file.

2. After reading and highlighting, I edit the markdown headers in Highlights (choosing the edit tab in the annotations window). I erase all but the primary author’s name and then add the Paper’s Citation and a Papers Link back to original file (copied from Paper’s Edit Menu). There is another quirk here. In Highlights Edit Mode, if you don’t leave a space between the markdown coding and the information you add, your file will be reset back to its original state, erasing your modifications.

3. Highlights has the ability to automatically look up DOI numbers. When it works, it’s great. It takes a single click to import a reference from the bibliography into your Paper’s Database. Unfortunately, this feature is flaky, especially with longer manuscripts. I often have to revert to my Launchbar scripts to capture the bibliographic information I need.

Once I’ve added the metadata I want to the master annotation file (and collected the references of interest), from within Highlights, I choose Export >> Devonthink. Highlights creates individual markdown files for each of the annotations. Each individual file contains the master file’s metadata. The data is copied to my Devonthink Global Inbox. I move the folder from the Devonthink Inbox to my Desktop and from there to my Annotations Folder using Launchbar.Highlights has significantly sped up the time it takes to process a manuscript. Using this method, I’m also having greater success with the “See Also” feature of Devonthink. I hope it works for you too.

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.

My Omnifocus Set-up - free webinar

I was honored to be a guest on Tim Stringer’s Learn Omnifocus to discuss my Omnifocus setup. I covered much of the material in My Omnifocus Set-up (Part 1) and (Part 2). Tim made the webinar available free on the Learn Omnifocus Website. Check it out!

Copied - a game-changing universal clipboard for all of your devices

It is grant season and thus it's been quite some time since I've written an entry. Today I want to talk about the program I'm using quite extensively for writing and social media. The application is Copied. Copied is available both for Mac and iOS. Copied is a universal clipboard application that makes information available on all your devices (with an in-app upgrade). The ubiquitous availability of your clipboard, in my opinion, is priceless.Some of the ways I am using Copied:

1. Capturing screen shots of my iOS devices for blog entries.
2. transferring information from programs such as Drafts to my Mac (without having to use an intermediary program such as Evernote)
3. Capturing information on my computer and transferring to my phone (e.g. addresses, screenshots, etc.)
4. Capturing images from the web—Copied automatically captures the URL of the picture and appends it to the clipboard entry (saving me the time it used to take to copy this information manually).
5. Quickly capturing the titles of references I wish to download after finishing reading a manuscript in Skim.
6. Capturing the references from a manuscript to be added to each of my extracted annotations.

I find a new way to use Copied every week. Copied has features (such as automated scripting templates) that I have yet to explore. Even without these unexplored features, Copied is a powerful addition to my writing toolbox - well worth the price.I’d be interested in hearing how others are utilizing this phenomenal app in their daily work.

Import Evernote into Ulysses

As you can tell from my past posts, I love the app Ulysses. As of this week, Ulysses became even more powerful with the ability to import Evernote files (although not in bulk). Check it out!

OmniFocus + Focus - Pomodoro Productivity

Combining Omnifocus and the Pomodoro Technique is an incredible way to get things done. Years ago, I used a program called Eggsellent. Eggsellent integrated seamlessly with Omnifocus ( flagged tasks in OF were added to the Eggsellent queue). The upgrade from OF to OF2 broke the integration, and the Eggsellent developer did not update his app.In searching for a replacement, I tried Vitamin R2 and Tomatoes. I settled on Tomatoes for its simplicity and visually pleasing interface. Tomatoes did not meet my needs. The only way to get OF tasks into Tomatoes was to drag and drop (or type). This was a far cry from the workflow I enjoyed with Eggsellent.From Tim Stringer’s Learn Omnifocus website, I found a Pomodoro app called Focus. Focus is one step closer to what I’ve been looking for since the demise of Eggsellent. The Focus Interface is clean, intuitive, and attractive. Although Focus does not autopopulate flagged items from OF2, it is easy to add a task using the “Share” menu. Timers and tasks are synchronized on Mac, iOS, and Apple Watch via iCloud.Focus is still missing some of the functionality I desire in a Pomodoro app. Besides missing automatic OF2 integration, there is no ability to add tags to each item. The only way to add metadata is via a text box. Add that to the relatively steep price ($19.99 for the Mac version, $7.99 for iOS).Despite these shortcomings, Focus is my favorite modern Pomodoro app and has replaced Tomatoes as my timer of choice. Give it a try.

Capturing Reminders with Apple Watch Using only your Voice

I received an Apple Watch for the holidays. I had avoided the technology until I was compelled by the features and capabilities. This year, with the release of the 3rd generation of watch software, the device finally made my list.So far, I’ve been most intrigued by the ability of the Watch to capture reminders. I merely say “hey Siri, remind me to…” and my item is automatically captured. I’ve set up Omnifocus to grab my Apple Reminders. So now, with only my voice, I’m able to capture my to-dos on the run using only my voice. I'm sure to use this feature both in my personal and professional (especially clinical) lives.

Highlights.app not ready for prime time

On recommendation of several people, I decided to try the annotation app, Highlights. Although I was intrigued with several of the features, after extensive use, I can’t recommend the app. The program still needs work before I could reliably use it in my writing workflow.I found two of Highlights features especially attractive:

1. The ability to extract each highlight or comment as its own markdown file.
2. The ability to underline references in the PDF and have those references automatically appended/linked to extracted notes.

I trialed Highlights for about a week. Ultimately, even with the intriguing features, The appnwas far too buggy for me to adopt.Here are some of the issues I faced:

1. References would not reliably link to a note. I could find no rhyme or reason for this behavior. Sometimes the feature worked, sometimes it didn’t. No matter what I tried, I was unable to remedy this issue. My attempt at editing markdown files led to frustration—my edits were often erased.
2. Even when the reference extraction worked, there is a bug that alters the markdown file, adding additional markdown to each reference. With many references, this bug makes each file unreadable.
3. I found no way to configure the order, type, and appearance of the metadata.
4. Extraction of figures from the manuscript were buggy and unreliable.
5. Metadata was impossible to change. Initially, I set Up the app to automatically retrieve metadata. Unfortunately, several of the paPers the software Retrieved had erroneous metadata. Once imported, I found the metadata impossible to change. Since I add the title, author, And other metadata to every one of my extracted notes, this was The fatal flaw that caused me to end my trial.

Although I am intrigued by several of the features of the Highlights App, I will continue to use my tried and true method of note extraction using Skim. I plan keeping an eye peeled for these issues to be fixed within Highlights. With some improvements, I could see the app becoming my Mac PDF reader of choice.

Skim Split Screen Workaround

When reading PDFs on my Mac, I use Skim. Although I love the program, Skim has one annoying quirk. I cannot select (or highlight) text in a split screen. This makes it difficult to highlight or download references in real-time.I found a workaround that is fast and efficient. After opening a PDF in Skim, I’ll select “Print” from the File Menu and then, from the bottom left drop down menu, I’ll select “Open PDF in Preview.” This opens a second editable version of the manuscript side-by-side with the original.Let me know how this works for you.

Voice Dream-Listening to Scholarly Information (PDFs) on the Go

Keeping up with current medical literature is a constant struggle. The amount of information in healthcare doubles every 5-7 years. To keep up, I try to take advantage of time that would be lost (for instance, while driving in my car). I typically use my commute time (a 20 minute drive each way) to listen to audio books, but occasionally I’ll “read” a scholarly manuscript using a PDF-to-voice conversion program.My favorite app for converting PDFs to sound is Voice Dream. I initially found this app while looking for a way to listen to web content (before the feature was built into apps like Pocket and Instapaper). I was pleasantly surprised when I found Voice Dream could also translate PDFs.I prefer Voice Dream to other readers because of its customizability. I’ve customized the voice speed, pitch, and volume. The readback speed takes some trial and error in order to find the proper speed to keep your attention and allow understanding.Voice Dream loads PDFs from Dropbox, Box, or Google Drive. I have a designated folder on Dropbox specifically for manuscripts I’d like to listen to. The interface for Voice Dream is intuitive. As the voice reads the text, the program highlights its current position in the text.Using this method, I recover almost 40 minutes of time that would otherwise be lost. Let me know what you think.

Airmail 3 - A Unified email Experience to Rule Them All

Several months ago I wrote about my discovery of Spark email. I wrote about what I like and disliked in the app. Although Spark wasn’t perfect, I preferred it to the built-in iOS Mail app. I used Spark exclusively on iOS for a month.But then, a reader wrote and told me I should check out Airmail by Bloop. I had tried an earlier version of Airmail, but was less than impressed. Regardless, I decided to check out what had changed in the latest version.When I read the updated features of Airmail along with the promise of a simplified unified experience across all devices, I decided to give it a try. I’m glad I did—I’ve used Airmail exclusively as my email client since mid-July.From the Airmail website:

Airmail 3 is a new mail client designed for El Capitan with fast performance and intuitive interaction. Support for iCloud™, MS Exchange, Gmail™, Google™ Apps, IMAP, POP3, Yahoo!™, AOL™, Outlook.com™, Live.com™Airmail was designed from the ground to retain the same experience with a single or multiple accounts and provide a quick, modern and easy-to-use user experience. Airmail is clean and allows you to get to your emails without interruption - it’s the mail client for the 21st century.

Beside the unified experience, I particularly appreciate the ability to customize every aspect of the email experience.In addition, Airmail supports services (the actions I use most commonly include saving attachments to Evernote or moving an email to an Omnifocus task).There are 4 customizable swipes. I  chose to customize this feature in the following manner:

1. short left swipe-DELETE email
2. long left swipe-bring up action menu
3. short right swipe-Archive
4. long right swipe-Snooze (message disappears to re-appear at a future time).

Another nice perk is the ability to synchronize accounts and settings using iCloud. This feature alone saved me tons of time when setting the app up on my Mac, iPhone, and iPad.I’ve been incredibly happy with Airmail over the past several months and don’t anticipate this changing. I hope you’ll give Airmail a try.