I have blogged about the custom Keyboard Maestro (KM)scripts I wrote to grab journal articles while reading scholarly information. Using these scripts, I merely highlight text in a PDF (usually a reference), invoke my KM script, and the PubMed or Google ScholarI now do the same thing using Launchbar Action Scripts. I set up three custom search templates in Launchbar’s Search Template Index:PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/?term=*Google Scholarhttps://scholar.google.com/scholar?hl=en&q=*&btnG=&as_sdt=1%2C34&as_sdtp=Research Gatehttps://www.researchgate.net/search.Search.html?type=publication&query=*Now, when I want to retrieve a reference, I merely highlight the reference in the PDF I’m reading and hit the Shift Key twice–this tells Launchbar that I want to do something with the highlighted text–by hitting tab and then typing the first few letters of Pubmed, Google Scholar, or Research Gate, then hitting Return, I tell Launchbar to pass the search string on to the publication web site. In order to find PDFs, I often have to repeat a search on more than one site. Launchbar makes retrieving PDFs fast and efficient. Check it out.
Embracing Evernote
Workflows evolve. A few years ago I was hesitant to use Evernote because of its proprietary nature. I was using plaintext to capture everything, but had to work out a complex syncing system to be efficient. Over the last year, I’ve overcome my fear and have increasingly built Evernote into my life. I started using it in so many ways, I finally subscribed to thePremium service. I’ve found Evernote to be a flexible and reliable tool readily available on all my devices — both for capture and to find information when I need it.
Here are a few ways I’m using Evernote:
Clipping Service
The first thing I installed when I started using Evernote was the Mac Clipping Tool. Using the clipping tool I easily capture, attach keywords, and annotate pages from the web. Using the “Share” menu in the web clipper, I copy a link to the note directly as a reference in OmniFocus or Calendar entries. When I’m on my iPhone or iPad I use the Action Button (the square with the arrow emerging from the top) to get items into Evernote.
Emailing notes directly into an Evernote NoteBook (premium feature)
I have transitioned my personal email client to Postbox. Postbox, unlike Mail.app, has an Evernote clipping tool embedded into the interface. Sometimes, I’m unable to use either of these methods and will choose to email a note into Evernote. To learn more about this premium feature, read the excellent overview of Evernote email features (including naming the file, placing the file directly into a specific notebook, or tagging the file with a keyword or reminder time).
I most commonly use this method when I’m answering an email, placing my unique Evernote email address and Omnifocus MailDrop Address in the bcc field of my email. Using this method, I can kill 3 birds with one stone (responding to the email, keeping the reference material, making an Omnifocus entry to keep up with the item).
Linking to reference material for Omnifocus or Calendar
Once information is captured Evernote, each note has its own unique URL. I use this feature extensively to link reference material to OmniFocus and my Calendar. I have different ways of linking depending on the situation.
By control-clicking on a note in Evernote and then selecting “More Sharing” I copy the web-based URL to my clipboard. I then paste the URL into the note field of Omnifocus or into the appropriate field of my Calendar. Then, even when I change devices, I have access to my reference material.
Another method of grabbing URLs is with Launchbar. As I mentioned, I now use Launchbar extensively. I can select a note in Evernote and then invoke Launchbar, then I select “Evernote – Copy Link of Selected Note.” This copies the URL of the slected note to my clipboard to be pasted into any other app.
Capturing Ideas in Evernote using Drafts
Evernote extends its great power by linking to many other applications. I’ve found capturing snippets of text into Evernote is even easier than the method I described a few years ago using plaintext.
I use Drafts on my iphone and iPad to capture / brain dump just about everything. Drafts is an essential program on my iPhone. Drafts allows me to capture without thinking about what app I need to open. Once the text is captured, Drafts routes the information wherever I choose. I wrote about one way I use Drafts to capture and process meeting notes.
When I want to capture an idea, I merely open Drafts and type or dictate my idea into the app. When I’m done, I route the information to Evernote using the following custom action:
The action automatically derives a title from the first line of the text and appends the date and time. Furthermore, it files the note in my “Ideas” Notebook in Evernote and tags the note with the keyword “Ideas."
The note ends up in Evernote looking like this:
When I get to Evernote, I append further information in the note as needed. I use IdeaX in the header so when I search for a list of my ideas, they are not mixed together with information I’ve gathered from other sources. If I search for a keyword(s), I not only see my ideas, but all the information I’ve gathered in Evernote—very useful.
Capturing Blog Ideas, Lyric Ideas, Quotes, and other Snippets in Evernote using Drafts
I use a similar scripts in Drafts to capture a whole host of other information on the go. Each class of information is filed into it’s own Notebook in Evernote. For example, here is the action I use to capture information for my blog:
By incorporating Evernote, I’ve greatly simplified many of my capture processes. I highly recommend giving Evernote Premium a whirl and trying out a few of these workflows on your own. You won’t be disapointed.
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 with my Voice
In my academic roles in the Duke University Human Simulation and Patient Safety Center I write a great deal. I write manuscripts, grants,white papers, and a whole host of other material. I’ve read the most efficient way to write a long document is to spew everything into a draft as quickly as possible, then go back and edit.Typing slows me down. The fastest way for me to “write” something is with my voice. I find it easier to adhere to this ‘draft first’ rule when I dictate using my voice rather than typing out a draft on my keyboard.Why is this? When I type, I tend to correct errors as they occur. Even worse, I try to polish each sentence on the fly (rather than powering through the entire document at one time). The constant editing interrupts my thoughts and makes slogging through an whole first draft extremely tedious.Lately, I've been using a workflow that takes advantage of the native iPhone’s dictation feature to “write.” This workflows has sped up my writing significantly by forcing me to keep moving forward while allowing me to write anywhere/anytime.This workflow is relatively easy to set up. Here is the software you’ll need.OmniOutlinerOmniOutliner is, you guessed it, an outlining program. Before I write anything, I use OmniOutliner on both on my iPad and on my Mac to plan my document. The Omni Group recently added the ability to sync to iCloud (currently a beta feature). Universal access to my outlines allows me to draft and rearrange my outline on the fly, regardless of location.ScrivenerThe next piece of software is Scrivener for Mac. Scrivener is an essential writing programs. That’s right, essential! If you don’t use Scrivener yet, stop reading and download the software right now.One of the advantages of Scrivener on Mac is it allows me to write in chunks. I can start writing in the middle of my project. When I sync the Scrivener project to Dropbox, I end up with a number of text files (each representing one ‘chunk’ of the Scrivener Project). Being able to write non-linearly from anywhere allows me to complete a draft very quickly. I am able to knock out sections of a document while in my car, walking between meetings, or anywhere else the urge to write hits me.Chunks of text in Scrivener may be moved around ad nauseum. I take advantage of the ability to move things around quite frequently. If I don’t like what I’ve changed, Scrivener has built in version control , so I can revert back to past drafts.Scrivener exports pieces of the project as individual files. Scrivener puts all these files in a “Drafts” folder inside the folder of your choice. These files can be txt, rtf, or other formats. I use text since I write in Markdown.DropBoxI set up a folder in my DropBox hierarchy called “Writing Sync.” It is here I synchronize my project between Scrivener and Editorial. Each new project gets its own folder.EditorialEditorial is a phenomenal text editor for iOS with a slew of built in features. Editorial allows me to edit documents written in Markdown and has a wholebunch of other features that makes it my go-to document editing software on iOS. Editorial, unsurprisingly, syncs with DropBox. I have Editorial point to my “Writing Sync” in Dropbox.Now that I’ve discussed the software I use, let’s set everything up.The WorkflowThe first thing I do is draft my outline in OmniOutliner. I typically do this on my iPad or my Mac then rearrange the outline until I'm happy. Once my outline is complete I export it as an OPML file.I create a blank Scrivener project, then import the OPML file into Scrivener. Importing the OPML populates the Scrivener project, preserving the hierarchy of the outline. Each bullet of the outline receives its own individual chunk in Scrivener.The next step is to set up synchronization of the Scrivener with Dropbox. Under the File Menu, I go to Sync->With External Folder….I make sure the back up before export box is checked and make sure that the project is exported as text. I select the “Writing Sync” Folder as the text file destination. I hit okay and the entire Scrivener project is exported to "Writing Sync" as individual text documents (Scrivener assigns a number to the front of each text file to keep them in order).On my iPad or iPhone, I point Editorial to my “Writing Sync” Folder. Within Editorial I can edit each of the individual text files. I open the file I wish to write/edit and use the dictation (Siri must be enabled) on My iPhone. Editorial immediately synchronizes the new text back into Dropbox.Once I return to my Mac I re-synchronize the project in Scrivener. All the files in Scrivener now reflect my writing from Editorial. One I've completed my first draft, I use this same back and forth method to edit.Once I'm happy with each of the chunks, I go back to Scrivener on my Mac and compile the whole document as a single Markdown file. I save this file a level above the “Drafts” Folder Scrivener created when syncing.I can access the full document using Editorial (or any other text editor) on my Mac or iOS device (I use Byword or Ulysses on my Mac) . Finally, when I'm done polishing, I export the document to Microsoft Word (or to the web). Using this workflow, I can write something in about 1/10 the time it used to take me with a keyboard. Although this method works well, it is not without a few annoyances. iPhones limit dictation to 30 second chunks. In addition, Editorial tends to chop off the last few words of a sentence after those 30 seconds expire. Because I’m working on segments of the overall project and can dictate quite a bit in 30 seconds, this is not a huge deal for me. When drafting, the key is to keep pressing forward.This workflow has literally changed to way I write. The workflow allows me great deal of flexibility and saves me a great deal of time.
Taekman Writing Workflow 2015
The early release of Papers 3 got a bad rap, and rightly so. My negative experience began as I imported my Papers 2 library into Papers 3. I had about 2500 papers, but only a fraction of these PDFs were imported properly. I am still recovering from these import problems--having to add each missing PDF by hand. Although importing was a issue early on, The makers of Papers, MekentosJ, now part of Springer Science+Business Media, worked hard to fix problems. I assume, with all the work on Papers, that importing has been fixed. My advice? Back-up your data before trying to import to Papers 3!
Although I had early problems, I can tell you that Papers 3 is pretty robust now. I recently used it to write and submit a full grant. I’ll say the app should be strongly considered if you’re looking for a reference manager / bibliography builder. If you’re interested in some of the changes in Papers 3, check out this entry.
With the release of Papers 3, all files and PDFs are bundled into a single container. Bundling makes syncing across computers more reliable, but indexing of individual files much more difficult. Unfortunatly, my Papers 2 workflow was dependent on indexing of single files. And thus, with the release of Papers 3, I had to revamp my writing workflow. That’s what I’m going to cover in this entry.
My current workflow has three parts: 1.organizing, 2. creating, and 3. writing/formatting
The software I use includes:
Papers3
DropBox
Hazel
Skim
Keyboard Maestro
Ulysses
Devonthink
Tinderbox
OmniOutliner
Scrivener
Pages or Word
Part 1: Organizing
Papers 3
Papers is used as my storehouse for all academic literature. I use Keywords and Smart Folders (akin to Smart Playlists in iTunes) to keep my literature sorted. In addition to the topic of each manuscript or book chapter, I use keywords such as "MustRead" that fuel my prioritized reading list. I tend to keep my library sorted by the date in the main window, but can easily search or sort my library in numerous other ways. My library is synchronized using Dropbox.
KeyBoard Maestro
Most people, while reading academic literature, find additional manuscripts they’d like to download. I’ve developed a series of KeyBoard Maestro scripts that simplify the download of these additional articles from Duke’s Library, Pubmed, and Google Scholar. As I’m reading a manuscript, I highlight the article I want to download and invoke my KM script. The macro copies the text string I’ve highlighted, goes to the appropriate web page (e.g. Duke’s Library), pastes the search string into the appropriate box, and hits submit. Thus with two keystrokes, I can find and download new PDFs I’d like to read. The new PDFs are sent to my “Downloads” folder. Then Hazel takes over.
Hazel
Hazel is a program that watches folders on my computer. When a file matches defined criteria, Hazel performs a script. I have a Hazel script watch for PDFs that contain the word “Reference.” When Hazel sees a file that matches, it launches Papers and imports the file into my library.
Skim
Despite the pleasing new main interface, Papers 3 highlighting leaves much to be desired. For reading and annotating scientific literature I use Skim (Skim can designated as the primary PDF reader in the Papers Prefernce menu). Skim has a robust feature set and is customized for academic literature. Oh, and it’s free! When I’m done reading and annotating, I export the Skim annotations to a PlainText file. I then use a KM script to name the the Skim Notes file to my convention.
Using another KM script, I parse the single notes file into separate text files (one for each highlight or annotation). Each file is named to convention and contains the text I highlighted in the manuscript, my own comments, and the full reference. All the individual notes are aggragated into a folder. I move this folder from my Desktop to the cloud so I can access it from anywhere. I call this my Literature Comments Folder. Now I move to Ulysses.
Ulysses
Ulysses is able to read files anywhere on my computer. I’ve configured Ulysses to point to my Literature Comments Folder so all my comments are available in an organized fashion. At this point I can add additional comments to my individual highlight files. The next step is to index the files in Devonthink.
Devonthink
Finally, I open Devonthink. This workflow has matured from what I discussed in this entry. I have a database that is solely used to index my scholarly reading. From the File Menu, I update the index (NOT import) of my Literature Comments Folder. Indexing this folder allows me to take advantage of the “Artificial Intelligence” of Devonthink, finding relevant information throughout my reading.
Part 2: Creating
Tinderbox
At this point I’m ready to start developing my scholarly work. I use Tinderbox (in Outline View) to generate a high-level preliminary outline. Tinderbox is a power-user’s application. I’ve only scratched the surface of its capabilities, but find it extremely useful early on to organize thoughts and find connections between what I’ve read and what I hope to write.
From within Devonthink, I review each of my comments. If I find something I want to include, I drag and drop the file (comment, reference, and highlighted text) into Tinderbox. Then, using Devonthink’s “See Also & Classify” command, I see related notes in my Literature Comments Folder . I drag and drop the additional comments into Tinderbox too. As I think of new ideas, it’s not uncommon for me to conduct a freeform search from within Devonthink to see which comments bubble to the top.
Once I have several dozen comments in Tinderbox, I find myself entertaining new thoughts, and often adjusting (or add to) my outline.
Another way I approach the creative process is to surf through interesting comments and move them one by one into Tinderbox without organizing them (usually in the Map View). Once I have a few dozen of these interesting quotes and highlights, I start to see connections between them, letting me further refine and organize my thoughts (and begin to develop and outline).
Once I’m satisfied with my outline, I’ll sometimes export to OmniOutliner for additional organization. But most times, I’ll export my outline directly from Tinderbox to Scrivener.
Part 3: Writing and Formatting
Scrivener
Scrivener is the place where the early versions of my manuscript are built. Scrivener imports OPML files from Tinderbox or OmniOutliner—each bullet of the outline gets its own content field. I do the majority of my early writing in Scrivener, attacking whatever section I feel like writing at the time. I use the Magic Citations of Papers 3 to insert my references as I write. Once I get words down on the screen, I often find myself tweaking the outline in Scrivener. This early phase, when I’m writing on the go, is when I yearn for the iPad version of Scrivener. Until that’s available, I’ll continue to use Scrivener’s synchronization with SimpleNote when I plan to write on my iPad.
When I’ve completed all the sections in my Scrivener outline, I’ll export everything I’ve written to Ulysses. I use Ulysses to edit and rewrite (in Markdown) until I think the work is ready for submission. As I’m importing and editing my paper in Ulysses, I make sure to have the document type set to Markdown (not MarkdownXL). MarkdownXL uses the curly brackets as an internal mark for annotations. If I use MarkdownXL in Ulysses, all of my Papers citations are formatted as footnotes—very annoying.
Word or Pages
I write and edit for several rounds in Ulysses. Ulysses for iPad makes this process more seamless and enjoyable. Unfortunately, when I’m done writing, I cannot format my bibliography in Ulysses. I have to export my file to Word or Pages. That’s okay though, I still have to format my paper. I use an old version of Pages (the new version of Pages still doesn’t allow bibliography formatting). Microsoft Word also works. To do this, I highlight all my text and from the Ulysses Edit Menu I select Copy as RTF (Word), then paste it in the word processing application. After my bibliography is formatted, I format the rest of the paper.
Finally, as the final check of my writing, I use a KM script to read back the text to me. I often find errors, even in this late phase of writing. Finally, I double check everything conforms to required format of the journal (or funding agency) and hit submit.
And there you have it: my writing workflow. As with most of my workflows it is continuously subject to improvement. For the time being this workflow has streamlined my writing. I hope it works for you too.
Tomatoes for IPhone
I’ve written about the use of the Pomodoro Technique and how it enhances productivity. I’ve explored many pomodoro apps, but my current favorite is Tomatoes by Dollaropath SRL. I especially like Tomatoes’ clean interface and how information syncs across Macs (using iCloud). That is the good news. The bad news? When working on Pomodoros away from my computer I had to rely on a different pomodoro app (there was no version of Tomatoes available for iOS). Since I was using a different app, all the data from my “mobile” pomodoros were lost.
With the release of Tomatoes for iPhone, I can now capture my pomodoros in a single application, regardless of device. Tomatoes syncs across Macs and iOS using iCloud. When I’ve wrapped up my day, week, or month I can graphically view my aggregated pomodoros or export all the data to Numbers or Excel for further analysis.
Although Tomatoes is my favorite pomodoro app, it is not perfect. Tomatoes can import native iOS to-do items, but does not integrate with Things or Omnifocus 2. Personally, I’d love Omnifocus integration (e.g. having a flagged item or a whole perspective from Omnifocus show up in Tomatoes). I’ll keep my fingers crossed for a future release.
Ulysses for iPad: Writing Nirvana
I use a great deal of plaintext and markdown in my writing. I’ve cycled through minimalist applications like Byword, iA Writer (and iA Writer Pro). A few years ago, in search of the perfect writing app, I stumbled upon Ulysses. Ulysses has powerful features for writers, but like many of the best applications, it keeps power features out of the way until you really need them. I like the app’s clean interface, how it handles (and emphasizes) markdown in a file, and especially the ability to organize multiple files across devices and cloud services. The Achilles Heel of Ulyesses has historically been its mobile implementation. There was no Ulysses for mobile devices. That is, until this week.
On Thursday, the long awaited iPad version of Ulysses was released. Ulysses for iPad has all the features that make Ulysses for Mac great. Some of you may balk at the price ($19.99 USD), but I believe it is well worth it. Check out my friend, David Sparks' (Macsparky), overview for more information.
In a future entry, I’ll talk about how my writing process has evolved to use Ulysses (in tandem with Papers and Scrivener) to tackle my large academic writing projects.
Cooking up Productivity: Pomodoro Technique and OmniFocus 2
Over the last month I have been experimenting with extending the usefulness of Omnifocus 2 (OF2) on my Mac. Of all the things I’ve tried, applying the Pomodoro Technique is by far the most effective.
The Pomodoro (Italian for tomato) Technique uses a timer to break down work into intervals. These intervals are traditionally 25 minutes in length, separated by short breaks. Four Pomodoros are followed by a longer break. To get a sense for the technique, watch this short video.
The original description of the Pomodoro Technique used a kitchen timer, but over the last several years Pomodoro Apps have become available. When I dabbled with Pomodoro in the past, my favorite app was Eggsellent. Eggsellent had a clean interface and, more importantly, would auto-populate flagged items from Omnifocus. Unfortunately, since the release of OF2, Eggsellent has been broken, forcing me to look for alternatives. The two applications I’ve spent the most time with are: Vitamin-R2 and Tomatoes.
Neither Vitamin-R2 or Tomatoes are completely right for me. Although both apps have quite a bit of flexibility in timer length and both have visual records of how I’ve spent my time, neither is automated enough for my taste. Neither app can pull information directly from OmniFocus like Eggsellent could. Vitamin-R2 has limited capabilites to check off completed activities in OF2, but that is the extent of its integration.
Since neither app is just right, the deciding factor for me was aesthetics. In this realm there is no comparison: Vitamin-R2 is clearly inferior to Tomatoes.
Here’s how the workflow in Tomatoes takes place: I slide an OF2 task into Tomatoes and tell Tomatoes how many Pomodoros the task will take. I click the timer to start and then follow the countdown either in my menu bar or in the app itself. The app records how many Pomodoros have been completed. I’ve been amazed at how competing against a clock solidifies my focus (and helps me to get more stuff done).
That being said, I’d really like an app that is functional, visually pleasing, AND can autopopulate items from OmniFocus 2. The best situation would be for the app to pull a particular perspective out of OF2. If it’s too complicated to pull a whole perspective out of OF2, I would settle for flagged items. Other aspects of the perfect app would be sharing tasks and statistics across computers (and iOS devices) and logging the Pomodoros in my calendar.
Give the Pomodoro Technique a try and let me know how it goes. If you’re a coder and are interested in developing the perfect Pomodoro application, please give me a shout.
Papers 3 Overview
Papers 3 has been re-written from the ground up. There are changes in virtually every facet of the program, from importing to matching manuscripts to storage and synchronization. Before I explain my workflow, I thought it would be important to familiarize you with some of these changes.
You can download a 30 day trial of Papers 3 and follow along with me. Papers 2 and 3 can exist side-by-side without altering your data.
Go ahead and install Papers 3. Once that’s done, let’s take a look at some of the preferences.
Preferences General:
I choose to open (and annotate) my manuscripts in Skim (as I did with Papers 2). For a short time, I experimented with the built in highlighting features of Papers, but they didn’t meet my needs.
Preference: Sync
I want my library to sync across my computers and iOS devices. Here, I’ve turned on Dropbox Sync and checked automatically sync new changes.
Preferences: Library
Here are my Library Preference Settings:
- (1) denotes the location of my Papers Library in Dropbox
- Hitting the Browse Button (2) places a virtual disk on your desktop that allows access to your entire Papers Library (via paper, author, year, etc)
- I keep the Copy files to Paper Library folder after import (3) checked
- I check Organize library folders by subdirectories (4). I use the convention Category Author Year
- I check Rename Files in Library Folder (5): I use the convention Author Title Source Year
Main Screen
This is the main Papers 3 screen. The terminology I use here is primarily my own–may deviate from what the company calls a specific area.
- The Library (1) organizes all the media in the program. My Collections includes both manually created folders and Smart Folders (folders created by metadata of the media. Shared Collections allows you to share selected folders with others.
- The Search Bar (2) allows you limit your searches or change the presentation of your Library
- The Filter Bar (3) lets you (from left to right) search for a document, view your library, view by Labels, view library by author, view by Type, and view previous database entries.
- The Viewing Pane (4) is where you view your media. I typically use the “Column” view, but there are other choices as well.
- Metadata (5) for the paper may be viewed (from left to right) by Overview, Information, Notes, or Activity
- Metadata Inspector (6) is where you view Metadata and related information
- PDF and Supplement Window (7) lets you visually see the first page of the actual paper as it exists in the library.
Annotations and Highlights in Skim
When I double click on an entry in Papers, the manuscript opens in Skim.
My Move to Papers 3 (End of Endnote Redux)
I was a big fan of Papers 2 as my manuscript and citation management software. After reading the early reviews of Papers 3, I was hesitant to upgrade and trepidatious about the future of the software. I went back and took another look at Sente, Mendeley, Endnote, and Zotero. In the end, I decided to stick with Papers.
Fortunately for me, despite the rocky start, the folks at Mekentosj have continued to work on Papers 3. About a month ago, I decided to make the transition from Papers 2 to Papers 3. This was not an easy decision, as changes in Papers 3 have forced me to revise major portions of my writing workflow. Although the transition was painful, I’m convinced what I have now is more robust and flexible than my previous system.
Over the next few weeks, I’ll write about my transition to Papers 3 (both Mac and iOS). I’ll cover the Papers 3 new interface, how I continue to leverage my Papers 2 data (despite the interface and data storage changes), and how I continue to integrate Papers 3 with Devonthink.
I hope you find my experience useful.
Writing Workflow: Have Your Mac Talk to You to Improve Editing
As I’ve mentioned several times before, writing is central to what I do. My research interest in the use of games-based learning and screen-based simulation has me writing constantly, whether grant applications, manuscripts, reports, concept papers, or blog posts.
An annoying fact about my writing: If I stick to visually proof-reading, I inevitably miss something. That’s why having the computer read back to me has become an essential step in my writing.
Having a Mac do this is quite simple—just highlight the text you’d like to hear, and Control-Click the text. Then under the Speech submenu select “Start Speaking.” To stop, Control-Click and under the Speech submenu select “Stop Speaking.”
If you’re like me, you’ll catch omitted words, duplicate words, syntactical errors, and the like. The only downside is if you stop the read-back, you can’t restart from the same spot—you’ll have to start from the beginning.
Because of this, I decided to develop and share two Keyboard Maestro scripts. The first, via a single mouse click, will select the current paragraph (regardless of where your cursor is) and read it back to you. The second, selects the whole document and reads it back. I use the default voice (Alex), but you can change the voice to whatever you’d like from within Keyboard Maestro.
Let me know what you think!
P.S. When you download script to your computer from Dropbox, you’ll have to remove the .txt from the file name.
Scrivener 2 (One of my essential writing programs) Half Off
Scrivener 2, by Literature and Latte, is one of my essential writing programs. Pick it up for $20 (55% retail price) at StackSocial through June 14. Thanks to Katie Floyd for pointing out this deal.
Medical Workflows on Mac Power Users Show 169
It was a great pleasure to be a guest on David Sparks and Katie Floyd’s Mac Power User’s Show 169. We covered topics such as writing workflows, electronic health records and iPads, and much, much more. Check it out.
TripIt: Travel Plans Made Easy
Although I don’t consider myself a road warrior, I do a fair amount of travel for my work. For years, my trusted travel partner has been TripIt.
TripIt is a web site (with apps for your iPhone, iPad, or Android) that aggregates all my travel information. Whenever I receive travel related information, I forward the email to the generic address: plans@tripit.com. TripIt processes the information from airlines, hotels, car rentals, etc., and combines them all into a single, easy-to-read itinerary (with confirmation numbers, phone numbers, times, etc.). The base site is free, but the Pro version is well worth the $49 per year. I’ve been a Pro subscriber for years.
Check out this video for more on TripIt.
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).
MyPhoneDesktop: Seamlessly Transfer information Between Mac and iOS Devices
I’ve written about the interplay between my Mac and iOS devices in several entries. The interplay between my iPhone, iPad, and computer are critical to my productivity. Recently, I discovered a program called MyPhoneDesktop that I use so often, it has made its way to the home screen of my iDevices.
Although I love my iPhone, I have trouble with the soft keys—they slow me down when I have to type things like URLs or text strings. If I wanted to transfer files, I would typically use Dropbox (or email) to get files from my Mac to my iPhone or iPad. But no more. After installing and configuring MyPhoneDesktop on both my iPhone and Mac, I can rapidly share information between my devices.
As an example, I can search for a contact on my Mac, then have my computer dial the number on my iPhone. I can send URLs, text snippets, or complete files from my Mac to my iPhone or iPad merely by dragging and dropping onto the app. Similarly, I can transfer pictures to my phone by dragging and dropping onto a pop-up receptacle that emerges from the right side of my screen. Perhaps best of all is the app's bookmarklet that passes a web page from the Mac to my iOS device through the push of a single button.
What’s the downside? I can’t transfer information from my iPad or your iPhone back to my Mac.
I use MyPhoneDesktop numerous times every day and you will too. Pick up a copy for $4.99.
PopClip for Mac
During my recent trip to Australia I had some time to catch up on listening / reading. Among the media were two MacPower User episodes. In Show 134, David Sparks and Katie Floyd covered Mac utilities. Although I was familiar with the majority, one utility was new to me: PopClip from Pilotmoon.
PopClip appears when you select text with your mouse on your Mac. Using Pilotmoon “Extensions” one can customize the app, then perform all sorts of useful actions on the highlighted text. Actions such as copy & paste, search, spelling, dictionary, shortening URLs, tweeting, etc. are all easily accessible through PopClip’s well-thought-out interface. I find myself using PopClip dozens of times each day. It’s well worth the $4.99 in the App Store.
Switching from SimpleNote to Notesy
In past entries I’ve written about how I rely on the combination of SimpleNote and nvALT to capture ideas, meeting notes, and more. I’ve been blissfully ignorant of the syncing issues between the two. I’ve had little problem with this combination, but apparently others have.
When I read that Brett Terpstra (the architect of nvALT) will no longer support SimpleNote, I knew it was time to find an alternative. For me, the choice was between Notesy and Nebulous Notes. Since I need my SimpleNote replacement primarily as a pass-through and for quick mobile searches, I settled on Notesy. I’ll reserve Nebulous for more in-depth tasks.
I also learned that Brett recommends DropBox syncing for nvALT–so I’ve moved my nvALT Folder back to DropBox. I backed up my folder and followed Michael Schechter’s directions to make sure I suffered no data loss.
The total time to make the switch was about 10 minutes.
Meeting Workflows: Processing Meeting Notes and Discovering Linkages
It was a great deal of fun to join my friends, David Sparks - MacSparky, Katie Floyd, and Brett Terpstra (hosted by Dan Miller) on stage at MacWorld Live to discuss my Meeting Workflow. The session was webcast live from the MacWorld site. Following the session, I received many questions as to how I process my notes once they’ve been collected. Here is what I do…..
As I mentioned, I write and capture all my notes in Plaintext (using Drafts on my iPad and iPhone and nvALT on my Mac). I covered the way I capture ideas (IdeaX) using TextExpander. I use a similar method for capturing meeting notes (MeetX), chunks of writing (ScribbleX), quotations (QuoteX), and random thoughts (ThoughtX). Using Simplenote Notesy, I’m able to keep my notes on my iPad and iPhone in sync with my Mac. A single folder indexed by nvALT serves as the repository for everything, regardless of their content. In a pinch, I can search my notes on my iPad or iPhone using SimpleNote Notesy, but the true power of this workflow is realized when I return to my Mac.
I have alluded to my love of Devonthink Pro Office. I’m especially fond of DT's ability to find related notes using its artificial intelligence. For the purpose of this workflow, I have a single database that indexes three things: (1) my collection of manuscripts (from Papers2), (2) my web clippings, and (3) my nvALT notes. My web clippings are added directly to my DT database, but my Papers folder and nvALT folder are INDEXED, not imported into the same database. Indexing in DT is done by choosing File:Index… and navigating to the folder of interest on your computer (this is only during the initial set-up). You will have to manually update the index your folders each time you add new information. This is quick and simple– done by choosing the appropriate folder in DT and choosing File:Update Indexed Items.
When I’m writing (or searching for information), I can select a particular note and find all related information in my library-whether it’s a scholarly article, a newspaper clipping, a web site, or a note I’ve taken. Often times, DT finds linkages for me that weren’t readily apparent. This speeds my writing process immensely and makes me look like a magician to my peers. I hope it works for you too.
Appended March 2, 2013: Read this entry on why I switched from SimpleNote to Notesy.
Soulver for iPad
I've written about Soulver for my Mac–a notepad calculator that allows you to mix words and numbers. And now Soulver is available on the iPad. Soulver is my favorite app for budget and grant planning. I can jot down my ideas line-by-line. If I make a mistake, I erase a single line (rather than starting over). Because I can mix numbers, calculations, and words, I am able to reconstruct my thoughts days, months, or even years later. And since Soulver syncs through Dropbox, I can share my work between my Mac and my iPad. The iPad version is currently selling for $2.99.