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.

The Long Road back to Launchbar

After listening to the Mac Power Users episode 286: Launcher Smackdown, I decided to switch from Alfred to Launchbar 6. I used Launchbar for years then switched to Alfred for its more pleasing user-interface. To be honest I never learned the intricacies of Launchbar. Back then I used it primarily as an application launcher. Boy, was I missing out.

After listening to my heroes (Katie Floyd and David Sparks) talk about how good Launchbar 6 was, I decided to give it a another try. I’m really glad I did.

I downloaded Launchbar and was up and running in a few minutes. I had to remap Command-Space (in Launchbar’s Preference Menu) to invoke Launchbar (I moved Alfred to Control-Space). I also decided, if I was going to switch back, I was going to learn the power users tricks—so I downloaded Take Control of Launchbar by Kirk McElhearnI. The book was excellent. I was able to finish reading it in about an hour (experimenting with the features as I read along). Within a few minutes I put together a new customized search template for PubMed. I am using Launchbar extensively while reading, and writing scholarly information (more on this in a later posts). Launchbar 6 is loaded with features. In fact Launchbar's mantra is “1000+ features, 1 interface.” I use Launchbar to act on files, invoke Services or  Keyboard Maestro scripts, collect and annotate text, and a whole lot more. I am especially enamored with one of the newer features called “actions.” Actions allow me to act on text or files copied on the mac or dropped onto the app. Using actions I can append information to a note, search Pubmed, or a whole host of other activities directly from the Launcher. Actions are improving my  everyday tasks as well as my reading and writing workflows. 

A tip of the hat to Katie and David for continually upping my game. Now that I’ve taken a deep dive into Launchbar 6 I know it is once again destined to become an indispensable application in my wheelhouse.

Writing and Reading Workflow: Batching and Automating Full-Text Retrieval

In my work at Duke University on simulation, games-based learning, and learning technology, I frequently read and write scientific information. I’ve developed a series of workflows to help me efficiently deal with information when writing papers and grants. In a previous entry I talked about how I try to batch operations, doing similar things at the same time. This entry will be about my workflow for reading scientific manuscripts.

I use Skim for scientific reading, typically using the bottom pane of the “Split PDF” feature to look at the title of references as I come across them in the body of the manuscript. On average, I’m interested in downloading about 10% of these references to my personal library.

Although I love Skim, one feature I have not been able to figure out is how to highlight items in the bottom split screen. Thus, I’ve created a workaround. Before I start reading an article in Skim, I create a note called “Get Manuscripts” As I’m reading, I merely record the references number of articles I want to fetch in my “Get References” note. Because I create this note first it’s always located at the top of my Skim Notes. When I’m done reading the current article and processing my annotations, I retrieve the supporting articles I identified while reading. 

To do this, I use a phenomenal program called KeyBoard Maestro. Keyboard Maestro lets me type a single keyboard command to trigger an entire workflow. One by one, I work through my “Get References” numbers, highlighting the title of each corresponding article. After highlighting each title, Keyboard Maestro does the rest (invoked by Command-Option-R).

Keyboard Maestro automatically  (1) copies my highlighted text, (2) surfs to the Duke Library literature search page, (3) pastes the text string into the appropriate field, and (4) submits the search. Thus, with a single key combination, I am able to download the full text of supporting literature. Once I find the full text I'm interested in (usually a PDF), I save it to my Download Folder, where Hazel takes over and imports the paper into my Papers Library.

If I'm not ready to retrieve the articles, I create an Omnifocus Action for each to be collected at a later time.

My macro is not limited to Skim, it works with any text I’ve highlighted, be it on the web, in a manuscript, or somewhere else. Here is a picture of the programming, but obviously, you’ll have to modify it for your own favorite full-text repository. Enjoy!

Addendum (January 14, 2014): If you’re searching at Duke, you’ve probably noticed the library changed its search interface. I’ve updated the Keyboard Maestro Script accordingly. It’s only configured to search for peer-reviewed articles. Download the script and import it into Keyboard Maestro (will only work for Duke Libraries).