Papers by Mekentosj - the End of Endnote

Information is expanding at an astounding rate–according to the Economist growing tenfold every 5 years. In healthcare, a great deal of new knowledge is disseminated through peer-reviewed publications. Over the last 10 years, healthcare publication has changed from primarily paper based, to a blended model heavy on digital documents. Print journals remain for one reason only–to generate revenue for the publisher….ah, but I digress. 

Managing an electronic library of information in healthcare is a challenge. In addition to manuscripts one must keep track of online web pages, reports, news articles, and more.Twenty years ago, we would dedicate massive filing cabinets to keep track of our photocopied article library. With the advent of electronic publication, most of our information is now stored in a digital format–most commonly Adobe’s Portable Document Format (PDF).

I use my digital library in multiple ways:

  1. as a reference for my own learning and recall (either new developments in my field, or information I searched that was relevant to a particular patient’s care), 
  2. as a repository of documents I’ll wish to cite in things I’m writing (e.g. manuscripts and grant applications) 
  3. to share information with colleagues, friends, or learners that have similar interests.

I have collected several thousand articles. Without a robust and flexible retrieval tool, I would have a difficult time finding and refinding information that was important to me.

Ten years ago I used a product called Endnote. Although state-of-the-art at the time, its features seem sorely lacking today. Endnote organizes your articles in a digital database that makes article retrieval easier. Its primary function, and the feature that made EndNote popular with academics, was its ability to format bibliographies. Although Endnote could store PDFs in its database, it only allowed you to search fields of data ABOUT the article, not WITHIN the article itself. As digital publication became the norm, Endnote’s features remained relatively static, until, unfortunately it no longer met my needs.

I began searching for alternatives. For a while, I used a program called Sente. Sente was more powerful than Endnote and I especially liked its annotation tools, but it suffered from a steep learning curve and a non-intuitive and non Mac-like interface.

It was about this time a colleague introduced me to Papers by Mekentosj.The software, now in it’s second version, is truly amazing.

Some of the things Papers2 can do:

  • serve as a repository of knowledge for any digital academic document I keep in my library (and plan to someday cite)
  • accept 85 different document types (including articles, books, media, web pages, patents, reports, etc). 
  • organize my papers iTunes style–including Smart Collections (special folders that automatically populate based on criteria such as date, keywords, etc) 
  • search metadata (data about the paper) as well as the words and notes within the text of the paper itself
  • automatically names pdf articles to the convention I specify  (I use Last Name-Title-Journal-Year)
  • searches publication databases like PubMed, Google Scholar, and the Web of Science all at the same time from a single unified window
  • allows me to drag and drop PDFs obtained outside of Papers (by email or on the web) into the application–Papers reads the document, retrieves metadata and renames the file to my convention
  • gives me a service to “print to Papers”–Papers reads the document, automatically retrieves metadata and renames the file to my convention
  • allows me to read, highlight, and make notes directly within the application–all of these elements become part of my searchable database
  • allows me to tag each manuscript with personal keywords (that help me better categorize and retrieve information) 
  • accepts (and reads through Optical Character Recognition) scanned documents
  • “Magic Manuscripts” allow me to cite any item in my Papers library in ANY program–and then automatically format a bibliography (like Endnote on steroids)
  • keeps track of the date I imported and / or read a manuscript 
  • synchronizes digital documents, folders, and Smart Collections with my iPad
  • sends references (and their PDF) via email with a single click
  • allows me to share papers with the Papers community

And the list goes on and on. Needless to say, Papers is an essential tool in my software arsenal. In future entries I’ll cover some of the specific ways I use (and enhance) this critical tool.

Download a free 30-day trial of Papers2 (available for Mac and PC) at the Mekentosj Papers web site.

OmniFocus Continued: Capturing Information in OmniFocus

In my last entry, I spoke about the power of Omnifocus. To get the most from the program, you must have easy ways to capture data. As I mentioned in my last entry, there are versions of Omnifocus available for the Mac OS as well as the IOS–I own them all. In this blog entry (and accompanying screencast) I’ll discuss the main ways I get information into Omnifocus.

Direct Entry

The least complicated way of entering a task is by manually entering it into the program itself. There are two ways to do this: (1) launch Omnifocus: Select Inbox: and type in the new Action (remember to frame the new item with a verb) or (2) Launch Omnifocus: select File: select “Quick Entry”: and enter the action.

Using the Quick Entry Box, you can capture a task and process it later, or if you expand the columns of the Quick Entry box (using the gear icon) you can type in the context, start date, etc at the time of entry. I try to estimate the amount of time it will take to complete the item at the time of entry.

If this is the first item in a new project, type in the name of the project in the Project column and then hit Command-Return. This will create a new project in the Omnifocus database. If you designate a Project while entering your item, it will be filed directly into that project. If you don’t, it will end up in your Inbox for later processing. Of all the ways to get information into Omnifocus, I find direct entry the most cumbersome.

Clippings

Clippings are incredibly handy and convenient. You highlight what you want, hit a key combination and, boom, Omnifocus launches and creates your Action item (with a link back to original item you highlighted). I use this method of capture Actions dozens of times each day. In order to get this to work you must set up your preferences in a specific way.

To set up Clippings go to the menu bar, and choose Omnifocus, then choose Preferences. In the Preferences menu click on the Clippings Tab. Define a Clippings Shortcut that works for you (I use the Command-Space-Period). Next you have to choose whether the clipped item shows up in Quick Entry (which allows you to do some additional quick editing) or whether you want the item dumped directly into your Inbox (I use Quick Entry).

Underneath the Copy Clipping to radio buttons are the different programs that work with Clipping. You can learn more about how Omnifocus will handle the clipping by highlighting each individual item next to the check box. I have all the programs checked. The most important selection is the final item: Any Application- make sure this is checked. You can then make and Action item out of information anywhere on your computer.

There is a special add-on for Apple’s Mail.app called the Clip-o-Tron 3000. Make sure this is installed (the installer is in the bottom right hand corner of the Clippings preference panel). The Clip-o-Tron let’s you highlight an email message and then use the key combination you designated above to automagically make a new Omnifocus Action. This new action contains the text of the email as a note AND a link back to the original email in your email database. This is my most common method of capturing Action items into Omnifocus.

If you’ve set up Omnifocus to synchronize (more on that in another entry)–the new Action will show up on all of your devices. Both Direct Entry and Clipping describe how I capture information from my MacBook Pro. Direct Entry also works on the iPad and iPhone. But I find myself usually using a third method to capture information from my iOS devices.

Capturing Information by Sending email

I’ve found I use my iPad more than my laptop these days. Unfortunately, capturing information is less convenient on my iPad. How do I get around this shortcoming yet maintain my productivity? By using email!

Open Preferences under Omnifocus menu bar and click on the Mail Tab. Make sure that the Mail Rule to create Omnifocus actions is checked. Next, look at the options under “Process messages having: radio buttons. I use the ”+omnifocus" before the @ sign option ( found it’s easier to have mail autocomplete a mail address than navigating to the subject line and typing). Next, you can choose the processed messages to be filed in a dedicated folder (I have a specific folder called at @Archive). If you leave this unchecked, the item will just remain in your email Inbox. Finally, (and critically) you must specify which e-mail addresses Omnifocus will accept mail from (I use all of my current e-mail addresses).

Now open Mail.app and select Preferences. Select the Rules Tab. Omnifocus should have placed a rule for you to edit. Here is how I’ve configured my “Send to OmniFocus” Rule.

 

Once configured, all I have to do is send an email to myself inserting +omnifocus just before the @ sign in the email address. When Mail.app is launched on my MacBook Pro, the item is automatically processed by Omnifocus and filed into the appropriate folder.

This is a handy method to use when you are reading email or a web page on your iPhone or iPad. I forward the email (or send a link to the web page) using my +omnifocus email address. This method  of capture is powerful, but what if I'm unable to safely send an email to myself yet want to capture something to OmniFocus (say, perhaps, while  commuting in my car or walking from one location to another)? It turns out that’s possible too, using Siri!

Using Siri to Capture to OmniFocus

This final method works only if you have an iPhone 4S with SIRI. As with the other methods, it takes a bit of configuration.

You must have Omnifocus installed on your iPhone. Launch Omnifocus on your phone and on the main Omnifocus Home Screen choose the Settings button (looks like a gear). Under Capture select the iCloud Reminders menu.

Make sure iCloud Reminders is turned ON. You also must enter your Apple ID and Password. Once this is configured, then hit the “Connect” button.

Siri understands two commands for OmniFocus. If I ask Siri to "Remember to..." the entry will be placed in my Inbox without an associated time. If I ask Siri to “Remind me to…..” do anything, for instance: “Remind me at 10am to call Dr. Smith about Patient Y’s operative plan,” a timed entry is placed in the OmniFocus Inbox and an alarm will go off at the requested time. What really happens is the entry is entered into Apple’s native Reminders App but when OmniFocus is launched, the reminder is transferred to your Inbox and the Apple Reminder is erased. The Omnifocus Inbox synchronizes with all your other devices.

The SIRI "Remind me to..." entry is context sensitive–if it’s before the time I specified, an alarm will go off to remind me to call today. If it’s after the time I specified, the alarm will be set for tomorrow.

I find this method of entry especially useful to capture items during my commute to and from work or when I’m walking between one location and another. In my opinion, this is one of the best applications of the SIRI technology–and has improved my productivity immensely.

Conclusion

I’m a heavy user of OmniFocus. In fact, Omnifocus is the hub of almost all of my workflows. During a typical day I’m inputting information constantly from many different sources. In this entry, I’ve covered the four most common ways I capture information into OmniFocus.

In my next Omnifocus entry, I’ll discuss how I organize and use Omnifocus in my daily work (and in the process discuss some of its strengths and limitations).

Until next time! Jeff Taekman

 

Why I Use Plaintext

As academic physician, a large part of my work involves writing. I write emails, meeting notes, drafts of manuscripts and books, blogs, ideas, grant applications, and more. I've owned every version of Microsoft Word for the Mac. But over the last two years, my workflow for writing has changed dramatically.

For me, writing can be very difficult. I find I write best with minimal distractions. I need to be in a position to get into a flow state and type whatever comes to mind. I’ve found it best to get the stream of ideas down on the page as quickly as possible, then come back later to edit. Software features, whether for formatting, editing, or reviewing often become a distraction. Over time, I've found I do my most productive writing in a program that offers few options (and thus very few opportunities for distraction).  Knowing this about me, you won't be surprised to learn that I have all but forsaken Microsoft Word (and Apple Pages) in favor of plaintext.

You might find this odd coming from someone who writes manuscripts and grants for a living. You're probably wondering how an academic can survive without Word? And why would a tech-savvy nerd like me choose something so basic as plaintext?

Please let me explain. If left to my basic inclinations, I might flail for hours trying to construct the perfect sentence. For a long time, this "perfectionism" would leave me stuck-often on the first page of a large writing project. Only recently did I learn to overcome this impediment. For me, the key to productive writing is for me to minimize distractions.  I need to control distractions in my environment, distractions on my device, and distractions within the writing program itself. Once I start writing, I try to keep my words flowing freely, saving the editing for my second (and third, and fourth) pass.

Word no longer met the demands of my workflow. I resented Word for its proprietary format, the size of its documents, its complexity, and the worst of all: auto-formatting. I commonly found Word getting in the way of my writing rather than getting out of the way and letting me write. Pages was not much better. And with either program it was difficult to keep versions synchronized between my Mac, my iPhone, and my iPad. After I wrote something I wanted the text to be immediately available on every device I owned.

I started looking for alternatives to Word and Pages. And there was a plethora of minimalist writing programs for the Mac and iOS to choose from. Most had only a few features–just enough to enable writing and to do minimal formatting. My favorite programs seamlessly synchronized to the Cloud, allowing me to write once, but access the text on any device. Because I write text bound either for a word processor or the web, I needed a single way to write in in words and in HTML. Plaintext combined with Markdown-a plaintext formatting syntax developed by John Gruber-allows me to write once and then move my words either to a word processor or to the web. Fletcher Penny’s MultiMarkdown adds many additional capabilities to Markdown and is especially handy for academics. If my note isn't going to stay in its native plaintext form, I usually run it through Marked-a program that imports Markdown/Multimarkdown and exports formatted text in the end format I desire (whether it's for a word processor or the web).

These days, I do the majority of my writing on my iPad or Mac using use a Markdown-enabled text editor. I use Word or Pages only in the very final stages of a writing project (after the bulk of the writing and editing is complete).

But there’s more. I spend about 30 minutes commuting in my car each day. I now occasionally use this time for “writing.” The addition of voice recognition to the iPhone 4s gave me the ability to dictate during my commute. I dictate into SimpleNote Notesy or the Dragon Dictation app on my iPhone. If I use Simplenote Notesy, the text automatically syncs using Dropbox and is immediately available on my Mac or iPad. If I use Dragon, all I have to do is mail myself the dictation and import the text into my writing application. I find myself drafting emails, letters, and even beginning long manuscripts while commuting. Then, when I arrive at the office, I just need to polish my prose rather than start writing from scratch.

Once I’ve written the document, plaintext is easy to share across operating systems (Windows, Mac, Linux) and devices-negating the need to buy proprietary software or other converters. Plaintext documents are tiny, taking up a fraction of the space of a proprietary word processing file. Plaintext is flexible-serving as notes in its native form, or as the early stage writing / editing platform for larger writing projects.

My current workflow for most short documents is to write or dictate them into plaintext (I use Writing Kit on my iPad, SimpleNoteNotesy or Dragon Dictation for dictation on my iPhone, and Byword on my mac). Although I can’t dictate Markdown on my iPhone, it’s a simple task to add once I reach my destination. I use Dropbox to keep all my notes in sync. If I’m writing a document, I can used Marked to copy my formatted text directly to Pages or to Word for final formatting. For a blog entry or web page I can export my Markdown document to HTML using Marked.

There are numerous writing apps for the Mac and iOS. I suggest you try several (most are $5 or less each) to find the best fit for your personal style. Brett Terpstra recently wrote a blog entry comparing the different features of writing programs for iOS. Features important to me in the editors were: (1) built-in TextExpander, (2) import Markdown and Multimarkdown files, (3) synchronizes to the Cloud or to Dropbox.

For large academic projects, I have a more complex workflow that includes several other tools. I’ll cover this more complex writing workflow in a future entry.

Cheers, Jeff

Appended June 17, 2012: I was taking a look at @MacSparky's Twitter feed. He recommended this blog post by @yuvizalkow : I’m A Failed Writer #13: Beyond Microsoft Word… Or Not on the same topic.

Appended March 2, 2013: Read this entry on why I switched from SimpleNote to Notesy.

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iPad Keyboard Conundrum

I've been astounded by folks who still insist the iPad isn't a great productivity tool. The early iPad was primarily for content consumption, but over the last 2 years, there has been a concerted effort by Apple and software developers to make it a phenomenal tool for creation as well. For me, a keyboard is the key to iPad productivity. With a keyboard and particular software (to be covered in future entries), my iPad 3 (err, iPad) serves as a replacement for my MacBook Pro 90% of the time.There are an expanding number of available Bluetooth keyboards out there. My personal journey started with Apple's wireless keyboard . Although this set up worked well, it was not that portable. I needed a separate bag to carry the iPad and keyboard-and found myself rarely going through the hassle of taking / pulling out my keyboard. As a busy academic physician that works both clinically and administratively, I am in need of a portable solution that would work in the operating room and the board room–thus I started looking at folios (case and keyboard contained in one).

A short time later, I settled on the Sena Leather Folio. Through reviews I summized the Sena had two disadvantages, 1. it was expensive and 2. it lacked a right-sided shift key. I decided to pony up and thought I could easily overcome the non-traditional keyboard. Boy, was I ever wrong. The lack of the shift key was my major complaint, but not the only one. I would never, ever buy one again. Besides the outrageous price, what were the problems?

Strike One-The lack of a right shift key-although I believed I could overcome this limitation, I have to admit it drove me absolutely crazy (and greatly inhibited my productivity). Having to consciously override years of (automated) typing behavior slowed my writing down considerably. I tried work-arounds such as writing while skipping the caps with the right hand-none worked. The cognitive effort needed to override my automated behavior greatly impacted the speed and quality of my work. Worse yet, when in the flow of writing, I would often fail to overide the urge to hit the right shift and would accidently type an apostrophe (the key on the Sena keyboard where the right shift SHOULD be).

Strike Two-The stand-I like to type while sitting in a chair or relaxing in my hammock (one of my favorite writing places). The Sena case has a single thin leg to help the iPad stand up in landscape mode. The design makes it impossible to type with the Sena in your lap; the iPad screen falls down.

Strike Three-the case enclosure-the iPad is bound to the Sena by a simple tab that tucks into the opposite side of the case. In less than a month, the tab became overly flexible, and the ipad constantly slipped about in the case (especially when propped up). This was not only annoying, but the case then tended to block part of the screen.

I can't emphasize enough the non-traditional layout of the Sena Keyboard will greatly inhibit your productivity! You've been warned.

When I purchased my new iPad earlier this year, I decided it was time to also upgrade my keyboard. Which brings me to the ZAGG Folio 3. I've owned the black leather folio 3 and keyboard for more than a month, and I can't say enough positive things about it. It is extremely thin, portable, easy to use and set-up. The case is designed to use the iPad primarily in the landscape mode, but the iPad can be removed from its holder and flipped to portrait mode if you so desire. The design of the case is such that it can be used in your lap, on a table, or even in a hammock. If you want to just read, the keyboard is thin enough to flip behind the screen, conveniently out of the way. A charge of the keyboard lasts several months I've charged a single time since my purchase- even with heavy daily use). Best of all, the Zagg Folio 3 has a standard keyboard (yes, with a right-shift key)-this alone has doubled my productivity in writing. The only complaint I have is the slickness of the leather case. I have not dropped it yet, but I fear it's only a matter of time.

The Zagg has become a critical piece of hardware in my productivity workflow. I suggest you order yours today.