Modification to Reading, Extracting And Storing Scholarly Information To Supercharge The Writing Process

In Reading, Extracting And Storing Scholarly Information To Supercharge The Writing Process, I wrote about how I extracted both highlights and full-text of entire manuscripts in order to give me granular access to information. Although I’ve continued my extraction of highlights, the extraction of full text (by highlighting the entire document) proved much too time consuming. Instead, I’ve been experimenting with an alternative that is much quicker (as suggested by Andrew in the comments of the entry)—saving the entire manuscript as single-page PDF documents. Here is what I’ve been doing.

After highlighting a manuscript in Highlights.app, I extract my highlights (along with color tags) to Devonthink Pro using the built in export function. By default, Highlights.app saves my extracted highlights files to the DTP Inbox. I move the folder from the DTP Inbox to my Desktop. Within the moved folder I make two new sub-folders: 1. HighlightsX and 2. PDFx. I then move the extracted markdown files to the HighlightsX sub-folder.Within Bookends, I export the annotated pdf to my desktop. There, I open the file with Adobe Acrobat (any app able to add headers and split documents will work).

In the left most header I put the Bookends citation (Bookends: Edit: Copy Citation), in the center I put the DOI number, in the right header, I put the Bookends link (Bookends: Edit: Copy Hypertext Link: Copy as Text). These headings are added to each page of the PDF. I then split the manuscript into multiple single-page documents. I save the split PDF documents to the PDFx sub-folder.

I then move the parent folder my Dropbox Writing folder and Index the folder using DTP. Within DTP I make sure both the main folder and the subfolders will have their tags included (option click on a folder in DTP and make sure “Exclude from Tagging” is unchecked)

.Although this method is faster—there are trade offs. The “Find Also” feature of DTP depends on the words in a document. A document with too many words dilutes the accuracy of the semantic search. A page of text has far more words than an extracted paragraph and thus is slightly less accurate in finding granular information. The other trade-off comes in the amount of text that must be read when searching. It is faster to scan a paragraph versus a whole page of text in a PDF. Regardless, the savings in time using this method far exceeds the trade-offs in accuracy.Let me know what you think.

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!

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.

Psychocybernetics and Agile: Goal Setting for the New Year

I'm a big fan of goal setting. I believe in subconscious mind and its role in achieving goals.Years ago I read PsychoCybernetics and strongly believe in its message. If you have not read the book, it essentially promotes the idea that our subconcious has a servo-mechanism that zeros in on wants and desires. The servo mechanism works both positively and negatively—our subconcious thoughts determining our ultimate target.The book convinced me many years ago I should maintain both short and long term goals and I should favor positive imagery and goals over negative thoughts and beliefs.Each year during the last week of December or the first week of January, I do a two-year sweep. I review the things I've accomplished over the previous year and the things I plan to accomplish in the new year. I review my short, medium, and long term goals and begin to build out what the current year will look like. I put my written goals into Evernote. I visually map out my year in MindNode.In addition to my goals, I also scheduled 30 day “sprints.” These are short term goals delving into new areas that interest me. Much of what I do is based on the Agile programming paradigm. An excellent reference on applying Agile to time management is the book: Getting Results the Agile Way.Here is a picture of my template for yearly planning:Now I'm off to do my review. I wish you a happy and healthy 2018.Sincerely, Jeff Taekman.

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.

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.

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.