I’d like to bring the latest update of BookEnds to your attention.This update fixed an error that would crash the Bookends when trying to obtain a reference (or link back to a reference in Bookends using a DOI link) from Highlights.app. The latest update fixes this error. Clicking on the reference link in Highlights now selects the reference in Bookends without having to modify the Highlights markdown file. This obviates the need to modify the Highlights markdown file as mentioned in this entry.The latest update also added a floating citation window to Bookends. Like Papers, the floating citation window is invoked using customizable key combinations. So far, I’ve cited using the floating window in Scrivener, Ulysses, and Highlights.app. It works flawlessly.Well done Jon and Sonny Software!
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:
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!
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.
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.
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.
I’ve found new ways to utilize my Apple Watch as a capture device. I previously wrote about how I capture OmniFocus tasks with only my voice.I’m using this same method to capture other information in Drafts and Day One. Both have Apple Watch applications.Most of the time, I capture items to Drafts on my Watch. I capture ideas, clinical questions, quotes, etc. My watch synchronizes the new item with my phone (in the Drafts Inbox). When I have a few minutes I can vector the new memo to the correct location using Action URLs.Occasionally, I will capture items directy to Day One (although this requires the Day One also to be open on my phone). I maintain multiple journals: Personal, Professional, 3GoodThings, Social Media, and Accomplishments. I’ll capture to Day One if I also wish to capture the location the item took place. Most of the time, I just capture to Drafts.Although I was a bit skeptical about the utility of my Apple Watch at first, it has become a useful tool both in my personal and professional life.
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:
- Capturing screen shots of my iOS devices for blog entries.
- transferring information from programs such as Drafts to my Mac (without having to use an intermediary program such as Evernote)
- Capturing information on my computer and transferring to my phone (e.g. addresses, screenshots, etc.)
- 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).
- Quickly capturing the titles of references I wish to download after finishing reading a manuscript in Skim.
- 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.
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.
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.
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.
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:
- short left swipe-DELETE email
- long left swipe-bring up action menu
- short right swipe-Archive
- 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.
Although I love the real estate of my iPhone 6 Plus, one of my ongoing dilemmas has been deciding what applications to keep on my home screen. I dealt with the dilemma by creating a series of folders. I never liked this solution since it looks cluttered and necessitates several clicks to get to any app.I recently rediscovered Launcher. Launcher gives one-click access to my most commonly used apps. Launcher works by installing widgets on the Notification Page of iOS (accessible by pulling down the menu from the top from any page). Launcher lets me launch apps, build communication shortcuts, access web pages, and much much more.I’ve built widgets for my most commonly used apps, clinical apps and links, texting and calling my family, and travel. I can move these launchers in and out of my access bar depending on the situation. For instance when I'm traveling I move my travel widget higher on the Notifications Page.I found this application incredibly handy. It's changed the way I configure my home screen. Spending the $2.99 to unlock the Pro features is more than worth the price.
Being a physician means a commitment to lifelong learning. In a busy clinical practice, two-thirds of clinical encounters generate at least one clinical question. In an average day the typical physician has at least 11 unanswered clinical questions. Only 40% of those questions ever get answered. Most of the questions are forgotten in the hustle and bustle of clinical care.In an attempt to improve my ability to capture (and answer) these questions, I've developed a new script for Drafts. This script uses the same concept as the technique I've mentioned to capture ideas, quotes, etc. This particular script saves information to Evernote but you could use Ulysses, DayOne, Wunderlist, or any other app you can program with an action. I chose Evernote since Evernote has the ability to find related notes anywhere in my collection. When researcing answers my question I capture those to Evernote as well-linking the question and answers in my Evernote database in perpetuity. Since Evernote is ubiquitous, the answer is available on my computer iPhone, and iPad.Here is how I approached this. First, I set up a new notebook in Evernote. I called this notebook "Clinical Questions." I then developed the following script in Drafts.Using this script it is now possible for me to quickly capture questions investigate later. I merely open Drafts and type or dictate my question, then hit the script. The question is logged to my Clinical Questions Notebook (along with date and prepended with tag ClinicalQuestionX).I’ve found myself using this script many times each day. I hope it helps you as well.Stats found on UptoDate: http://goo.gl/BDBqmH
I have been quite impressed with the Scriver iOS Beta--it's capabilities far exceeded my expectations both on my iPhone and iPad. It has already simplified my Writing Workflow. I'm not alone in my exuberance. Check out this glowing review. The wait for The official release is almost over....the official date Is July 20 at a price of $19.99. There will be a simultaneous release of a new version of Scrivener for Mac.
A couple of months ago, I was feeling the age of my first generation iPad Air and decided I needed to upgrade to an iPad Pro. I was torn between the larger 12.9 inch model and the smaller 9.2 inch model. Although I was attracted to the portability of the 9.2 inch version, in the end I bought the larger model. I decided to go with the larger model for a variety of reasons: 1. When reflecting on how I used my technology, I found when I had a task to do, I'd often forgo the iPad Air and just use my iPhone 6 Plus, 2. I wanted the best support for my extensive use of the Duet App (the larger screen giving me more portable dual screen real estate), 3. It was becoming increasingly difficult for me to read and annotate PDFs on the smaller screen.I purchased the iPad Pro (along with a Logitech keyboard and Apple Pencil) and have not looked back. One of my favorite unexpected uses of the iPad Pro is the ability to write with the Apple Pencil. In addition to Mindfulness and meditation, I am a true believer in the process of Morning Pages, a journaling technique that espouses the power of long-hand writing in the creative process. Up until the time I bought my iPad Pro, I was using a LiveScribe Pen to do my daily writing. No more!I have been experimenting with various writing apps including: GoodNotes, Penultimate, and Notability. Despite the more feature-rich environment of GoodNotes and the versatility of Notability, I find myself favoring Penultimate, primarily for its ease-of-use and automatic Evernote synchronization. I'd love to hear what your favorite handwriting app might be, and how you're using the handwriting capabilities of the new iPads.If you are not yet writing your own Morning Pages, I hope you'll give it a serious try.
Meetings are unavoidable in academics. For busy professionals, finding a time to meet can be a daunting task. Although apps like Outlook have built in scheduling features, few use them. One major limitation; Outlook's scheduling features only work for individuals using the same corporate domain.Previously, I wrote about my love of Sunrise Meet--a fabulous add on to Sunrise that smoothed the task of scheduling meetings. Sunrise was purchased by Microsoft and, unfortunately, the app will soon be shuttered. Thus, I went on a quest to find a Sunrise Meet replacement. I'm happy to report I found great alternative: Free Time 2Free Time 2 is a standalone app for iOS. The interface is clean and intuitive. If I receive a meeting request, I merely open the app and surf to the potential day(s) of interest. Each day displays a list of appointments along with my free time.I select as many potential meeting times on as many days as I’d like to propose.I then hit “Share,” opening the Action Menu.I choose what app I’d like to share my availability. Free Time formats the list of the potential dates for me. Here is an example in Spark.Free Time 2, in many ways, outshines Sunrise Meet. I use Free Time several times each day to schedule 1:1 meetings. Now if only there was an app that could seemlessly handle multi-person scheduling. Enjoy!
eMail is the bane of everyone's existence. Although I’ve been pretty diligent about reading email on the go, a problem I frequently faced was the issue of “skimmed emails”-those emails I read on the go but failed to immediately process. Later, when I returned to my Mac, I often missed the skimmed email because each appeared "read." Unfortunately, until recently, I had not found a suitable solution to this recurrent problem.I am a big fan of Macsparky. One of my favorite features on David Spark’s Web Site is the sharing of user’s home screens. In a recent post, I saw Brett Kelly (Website)(Twitter) mention Spark by Readdle and decided to give it a try. I have to say I’ve been incredibly impressed. Spark has completely replaced Mail.app on my phone and iPad. I can’t imagine going back.Spark is one of those apps that is a delight to use. The developers paid a great deal of attention to user-interface design. Even now, several weeks into my exploration, I continue to find subtle features that really do live up to Readdle's promise to have me “Like Your email Again."Spark has almost completely eliminated the Skimming problem on my phone. I now process 98% of my emails as I read them on the go. My Inbox has remained essentially empty since I started using the App.A few minor suggestions that could make the program even better: 1. the ability to add actions to swipes (ala Drafts) and 2. the addition of other gestures (taps?) that would further enhance the number of customizable processing options.Spark is now my iOS email client of choice. I hope you give it a try too.
I have become a big fan of the new Google keyboard, Gboard. I've been using this keyboard for IOS over the last week. During that time, Gboard has become my keyboard of choice supplanting the native Apple keyboard. I particularly like the ability to glide type and the ability to look up information on Google without leaving the current application. I’ve found emoji links, GIFs, and image links less useful.The only three drawbacks I have found include:1.losing the ability to dictate, 2. losing the ability to enter passwords, and 3. the fact that GBoard does not understand Apple Keyboard Shortcuts.For more information check out the Cult ot Mac article. Download Gboard and give it a try. I think you'll be pleasantly surprised.