Deckset: Rapid Presentation Generation using MarkDown

My workflows have changed since I wrote my entry: “Why I Use Plaintext” in June 2012. The entry was about avoiding the distraction of Microsoft Word and Apple Pages while writing. At the time I wrote the entry there was no Ulysses. Now I use Ulysses for almost all my short-form writing. In 2012, there was no iOS version of Scrivener. Now I use Scrivener for all my long-form writing. Although technology has changed, some things have not. I still dislike bloated software packages that get in the way of my final goal. I still love Plaintext / Markdown.There is another requirement of my job that relies just as heavily on bloated software-presentations. Speeding up the development of a presentation is the focus of this entry.Presentations are used throughout business and academia to transmit ideas. Some influential thinkers, such as Edward Tufte, argue bulleted presentations shouldn’t be used at all. The reality is that presentations are deeply ingrained in business and academia. Many presenters rely too heavily on the glitz offered by the software at the expense of content. It’s easy to get lost in software features—spending hours tweaking backgrounds, transitions, and text placement.Which brings me to Deckset. Deckset is an amazing application for iOS that converts Markdown files into presentations. As this review of Deckset 1 in Macworld says: “It’s designed for the average person who needs to make beautiful slides without the muss and fuss of Keynote or PowerPoint.” With the release of Deckset 2 and its outstanding features, the application has become my go-to application for rapid preparation of presentations. Because Deckset uses Markdown, I find myself concentrating less on making my slides look attractive and more on content. Deckset works seamlessly with Ulysses, allowing me to quickly edit my presentations on my phone, my tablet, or my Mac. (You can use any text editor with Deckset. If you plan to use Ulysses, check out these helpful tips).I recently used Deckset to develop a new 30 minute presentation. I estimate the presentation took about 1/4 the amount of time to develop versus Keynote. The cost for Deckset 2 is $29 (with educational discounts available).Here is a link to the Deckset manual.

Bookends Adds Floating Citation Window

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!

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.

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.

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.

Travel Receipt Workflow

Here is a handy workflow to keep track of your reimbursable / billable expenses on the road.Set-up:

I have an Evernote Notebook that is used solely for professional receipts. This notebook is named “Receipts_Work”. I’ve set up an If This Then That (IFTTT) Applet to send an email when the notebook receives a new note.When I receive a receipt on the road, I immediately scan it with Scannable then save it to my Receipts_Work Notebook. IFTTT monitors the Receipts_Work Notebook. When the new note is detected, it automatically sends an email to both my assistant and my Omnifocus Maildrop address (so the item is added to my Omnifocus Inbox).After my trip, I can go back to my Evernote, select all the receipts/notes from my trip and make a “Table of Contents” using a single button push in Evernote.This workflow simplifies management of reimbursement receipts. Hope it works as well for you as it does for me.

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.

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.

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.

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.

Capturing Clinical Questions Using Drafts and Evernote

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