WiPPP moved to Squarespace

Wordpress was the original blogging platform for WiPPP, but over the past year, I became increasingly disheartened with the classic blogging tool. Maintaining my site in Wordpress became a chore. I prefer developing content to maintaining a web site.

Several years ago, I decided to run my online professional portfolio, jeffreytaekman.com from Squarespace. I have been so impressed with the ease-of-use and support that I decided to transition WiPPP to Squarespace.

Over the next several weeks, you will notice a new format for WiPPP. The transition has not been pain-free. Although Squarespace's import tool worked amazingly well, many of the backlinks to historical posts have broken. Please bear with me while I correct these issues. If you notice a broken link or other problem with WiPPP, please send me a message so the issue can be fixed.

Thanks again for reading.

Sincerely, Jeff Taekman

Automating the Organization and Accessibility of Academic Literature: Bookends and Devonthink Pro

I wrote about Sense-making of the Academic Literature back when I was using Papers. My old workflow required Keyboard Maestro to extract abstract information to Tinderbox. Although Tinderbox is great for visually organizing your notes, it can’t compare to the search capabilities of DevonThink Pro.Since switching to Bookends, I’ve found myself spending less time in Tinderbox and even more time in Devonthink. I’ve made heavy use of a particular built-in Devonthink Template that automates the migration of abstracts from Bookends to DTP (with a link back to Bookends). Once imported into DTP, these abstracts can be parsed using smart folders (enduring searches) that make your literature library a dynamic resource for writing.I have a single DTP database that has indexed the various folders critical in my writing process (e.g. PDFs, extracted notes). In DTP, I’ve organized these folders into a “zz-Inputs Folder”. As you can see below, a sub-folders of zz-Inputs is an “Abstracts Inbox.” When I set up this folder in DTP, I made sure the folder WAS NOT excluded from tagging (this is done by option-clicking on the folder and making sure “exclude from tagging is UNCHECKED).When it’s time to transfer abstracts from Bookends, I first click to select the Abstracts Inbox folder in DTP.I then open up Bookends and sort the fields by the “Added” Column. I like reverse chronological order so I can see the last date I imported abstracts. I highlight all the new manuscripts in Bookends.I then move over to DTP and select the Data:New From Template: Education: Reference (from Bookends) menu item. DTP grabs all the highlighted abstracts from Bookends.The imported information includes Author, Title, Year, Abstract, and Keywords. The template also includes a link back to the publication in Bookends. Finally, there is a field for me to add my own comments to the new DTP file.Once the abstracts are imported into DTP, I make sure to index the folder so the new information is included in search. Now that the information is in DTP I am able to take full advantage of its search functionality and artificial intelligence.I make extensive use of Smart Searches in DTP. Using Smart Searches, The abstracts are automatically sorted into folders.For most topics I have two Smart Searches:

1. as shown below that includes the search criteria AND searching for the tag “Abstracts Inbox” we talked about earlier—this finds only abstracts relevant to the search,

2. only the search criteria—this returns ALL information in the database (including abstracts, PDFs, and extracted text as described in this entry).

In DTP, I bring up the Search Interface (Tools: Search….) and type in my search criteria. By default, in the Search Interface, DTP will search across all databases. Notice on the left hand side I have limited the search to my Writing Database. This returns ALL matching information ONLY in my Writing Database. I’ve color coded information extracted from articles using Highlights (for instance, a blue highlight is a direct quote). I can further limit the search by clicking on the “Advanced…” Button and adding additional criteria (e.g. tags, file types, words such as “blue,” etc.).Once I’ve found an abstract that interests me, I locate semantically similar information by highlighting the abstract in DTP and then clicking on the “See Also” button (the Magic Hat).Using this method, all the information I’ve collected (both read and unread) is easily accessible. I use this method extensively when writing. Please let me know if you find it useful too.

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!

Reading, extracting and storing scholarly information to supercharge the writing process

Bookends has completely replaced Papers.app as my citation manager. Despite this change, my method of information gathering has changed little since I covered the topic, except for one major addition. I am now finding the majority of information through qxMD Read.My workflow for extraction of annotations differs a bit from when I was using Papers. I now use the combination of Bookends and Highlights.app to extract each of my annotations and notes as separate files. In addition, after highlighting, I’ve been extracting the entire manuscripts in 1-4 paragraph pieces.The whole purpose of extracting annotations and full text from each manuscript is to gain granular access to the information I’ve read. Through its "see also" feature, Devonthink can identify information I’m looking for. But more importantly Devonthink finds related content based on the context of my original query.After importing a manuscript into Bookends, the document becomes available on all my devices. Bookends outshines Papers in its built-in annotation tools as well as its seamless syncing between iOS and Mac.

My current preference is reading PDFs on a 12.9" iPad Pro along with an Apple Pencil. In a pinch, I’ll annotate on my iPhone. On my first pass through an article, using Bookend's built-in tools, I highlight annotations and jot notes in green. I use blue to highlight quotes I wish to use verbatim. When I’m finished annotating, I add the keyword RFP (ready for processing) to the manuscript in the Bookend database.

I have a Smart Folder set up in Bookends that finds the Keyword RFP. Uzsing this method, I can batch process multiple PDFs when I get to my Mac.When I'm ready to extract the information from the PDF into my Devonthink writing database, I export the PDF to my desktop and append the exported file’s name with FT (for fulltext).On my desktop, I open the file with Highlights. I use Copy Hypertext Link:Copy as Text from Bookends, and then open the “Edit” Tab in Highlights. Using use the text URL copied from Bookends to make a markdown link back to the Bookends Reference.When I export my annotations to Devonthink, the URL link will be appended to each file. Clicking the link within any extracted file takes me directly back to the reference in Bookends.I then turn my attention to Highlights.app. I make sure the annotations color preference is checked in Highlights.app. When checked, this preference will append the color of the highlight in each note.

Within Highlights, I use yellow to mark up the entire document over the top of my previous annotations. I highlight in 1-4 paragraph chunks. I also highlight the text of each table and figure.Once I'm done highlighting the entire paper, from within Highlights.app, I export my annotations to Devonthink from the Highlights.app menu. The annotations are saved as individual files to my Devonthink Inbox. I move the folder from the Devonthink Inbox to my desktop and then use Launchbar to move file from my desktop to my annotations folder. I put the desktop PDF in the trash, replace the RFP keyword in Bookends with DTx to remind me I've extracted the paper.

Since I’ve set up my Devonthink database to index this folder,the next time I launch Devonthink, the new information is catalogued and available for writing. The new information is also transferred to Devonthink ToGo to use while writing on my iPad.Using the Artificial Intelligence of Devonthink. I can quickly find related information. When I find an item in my database I want to include in my paper, clicking the link in the annotation takes me directly to the paper in Bookends.app.Using this method, I'm able to take full advantage of the Devonthink AI. Queries within Devonthink simultaneously find annotations, chunks of text and full manuscripts related to my search. I find this workflow invaluable when writing scholarly information.

***This workflow has been modified from here to the end-Please see Modification to Reading, Extracting And Storing Scholarly Information To Supercharge The Writing Process to see what I do instead.***

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.

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.