Meeting WorkFlows: Efficiently Capturing Meeting Notes

In academics, like every other corporate entity, meetings are a necessary evil.

I’ve tried all sorts of solutions for capturing notes and action items from my meetings. For many years, I would haul my MacBook Pro into the room, relying on a slew of software invoked through Launchbar.

Next, I transitioned to the cool LiveScribe Echo. The Achilles Heel of Smart Pen Technology for me, true to the physician stereotype, is that I have awful handwriting. Most of my handwritten notes were illegible. To make matters worse, sending handwritten notes to OmniFocus was a kludge.

Recently, I’ve been carrying my iPad + Zagg Folio to meetings. Although convenient and portable, I have continued to depend on a slew of software to capture my notes and to-dos. None of my methods were standardized; my notes would constantly get lost.

This inefficient workflow was why I was so interested in the 512 Pixel post, The Capture Form. The author developed a standardized PDF form to capture meetings. But that wasn’t what I found interesting. It was the very last line of the article, with a link to a TextExpander version of the form.

I riffed on his work and developed a new workflow for my iPad + Zagg that I’ve been trying out.

My workflow starts with setting up the following TextExpander snippet:

MeetX - Untitled - %Y-%m-%d at %H:%M

 

ATTENDEES:

JMT

BACKGROUND / REFERENCE:

 

NOTES:

 

ACTION ITEMS FOR ME:

 

ACTION ITEMS FOR OTHERS:

 

The first line automatically names the note as a meeting, appending the current date and time. I use the title "MeetX" to help me with search. I know if I search for MeetX I'll only see my meeting workflow notes (instead of every document that had Meet or Meetings). All that's left to do is fill in the title. Since I synchronize TextExpander between my Mac, iPad, and iPhone using DropBox, my snippet is immediately available on my all my devices.

The second part of the set-up involves OmniFocus and their Mail Drop service (note: in order for this to work you have to sync OmniFocus with the Omni Sync Server). If you haven’t done so, log onto the Omni Sync Server, and apply for the Mail Drop Beta (when I applied, I received my invite in a matter of minutes). Once accepted, you set up a unique email address that is your direct link to Sync Server. To learn more, check out the Omni Mail Drop story at MacSparky.

When I want to take meeting notes, on my iPad, with TextExpander running, I launch Drafts. I expand my snippet (in my case by typing “.mtg”), fill in a title, and am ready to go. If I’m preparing for a meeting in advance, I type in my reference material under the appropriate heading, then fill in the remaining fields during the meeting. Most days, I get started with my note taking immediately when I enter the room.

When the meeting is over, within Drafts, I forward my notes to Notesy Simplenote. Since I’ve set up Notesy to synchronize with NValt on my Mac (as I wrote about previously), my meeting notes are immediately available and searchable on all my devices.

If personal to-do items came out of the meeting, I have another step. From within Drafts, I select “forward to email,” type out a subject name, then email the note to my personalized Omni Mail Drop address. When I open OmniFocus, the item is waiting for me as an Action in my Inbox. Even cooler, the complete meeting text is available in the "Notes" field . If there are multiple actions embedded in the original meeting notes, I spend a few minutes processing the set into single unique actions.

An alternative: from within Drafts select "Send to Omnifocus as note" (of course you have OmniFocus installed on your iPad for this to work). Drafts will launch Omnifocus and the notes of your meeting will be placed in the appropriate section of a new action. The only thing left for you to do is type in the name of the action.

This workflow has helped me immensely. I now have an efficient, standardized, searchable, multi-device method for recording and retrieving my meeting notes.

I’m really excited about this workflow–I hope it works for you too. Let me know what you think.

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

Workflow: Capturing Ideas

Ideas are my lifeblood. Whether ideas for writing projects, grants, or to-dos, I need a simple method to get the ideas out of my head and into my system. An idea might come to me during a meeting, in the car, or on a walk. My system has to be fast, ubiquitous, and flexible. The less thought I have to put into capturing my ideas, the better.

Over time, my workflow for capturing ideas has evolved. You won't be surprised my system revolves around plaintext.

Here is the software you'll need for this workflow (you may also want to read my previous entries on why I use plaintext, Launchbar, and Drafts):

TextExpander allows me to type short key combinations (called Snippets) that expand into words, phrases, or even pictures. I use TextExpander constantly to type things like my email address (.hm expands to my home email, .wm expands to my professional email). I use similar combinations for my home address, my city, state, and my email signature. TextExpander is available for iOS devices (called TextExpander Touch) and is integrated into an increasing number of iOS programs. Under preferences, I choose to keep TextExpander Snippets synchronized using DropBox. I highly recommend this--identical snippets are then available on your Mac, iPhone, and iPad only needing to be entered once.

One must also have nvALT - Notational Velocity Fork installed on your Mac. Notational Velocity Fork is a special version of Notational Velocity that was developed by the genius, Bret Terpstra. It allows me to create text notes seamlessly and has a lightning fast search function. nvALT launches and I just start typing. Whatever I type becomes the title of my new note (after I hit return) while simultaneously searching the nvALT database for matching text strings. Hitting return finalizes the title and move the cursor down to a full note area. It's very fast. You need to check three settings in nvALT. First, be sure to set the "Read from Notes" drop-down menu to your desired folder. I synchronize to my nvALT folder in DropBox. Second, under the "Synchronization" Tab, make sure SimpleNote synchronization is OFF. Finally, under the "Storage" Tab, make sure you're saving as plaintext (not as RTF or HTML). If you choose this set-up, you won't be able to encrypt the nvALT database, but the trade-off in accessibility for me is well worth the price.

Next, make sure you have Simplenote Notesy installed on your iPhone and iPad. Notesy is a note taking program that synchronizes between your Mac and iOS devices using DropBox. Make sure Notesy is configured to synchronize with your nvALT folder in Dropbox hierarchy. I use Notesy as a conduit and for searches, but I rarely use it for writing.

The final programs you'll need are Drafts for iPhone and Drafts for iPad. As I discussed in my previous entry, Drafts is my go-to note taking app and has a place on the coveted home-screen of both my iPhone and iPad. I can get information entered quickly. Only after the information is captured, do I need to decide where to route it. Drafts gives me dozens of possibilities that I can personalize to show or hide.

IDEAS WORKFLOW: when sitting at my Mac and and idea hits me I invoke Launchbar (hitting Command-Space), type nv then return--launching nvAlt. Depending on what the idea is, I use TextExpander snippets. For instance ".wix" automatically types the following: WiPPPx - Untitled - 2012-12-10. I have a similar snippet for project ideas ".idx" expands to IdeaX - Untitled - 2012-12-10, and many others as well. All I have to do is change the "Untitled" to something descriptive, hit return and start typing. My idea or writing snippet is captured to nvALT (and is thus searchable via Spotlight, nvALT, or any other search utility I prefer). Because I've set up synchronization these idea files are available on my iPhone or iPad regardless of location.

If i'm on my iPad or iPhone and want to capture an idea, I use Drafts. Once I've completed the thought (using typing or voice entry), I must enter a title. Since Drafts is TextExpander Touch enabled, I can use my same Snippets to name the idea to convention (make sure TextExpander is open on your iPad or iPhone for the text expansion to work). I then route the completed Drafts note to Notesy (via the Drafts interface). It is saved, synchronized, and available on all my devices, all the time.

I can then search and find single or multiple ideas using the nvALT search interface. If I type "IdeaX" in the nvALT search box, ALL my ideas are returned in neat order. If, instead, I'm searching for a specific idea, I can be more explicit with my search terms, finding related items or even a single item.

Although this workflow takes a bit of set-up, the payoff is immense. Over time, I have accumulated hundreds of potential projects, text snippets, and more using this method. Many of them would have been lost, had I not had a quick and convenient way to capture them.

I hope you find the workflow useful.

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

 

Core Software for the Mac: Default Folder X

I use my computer and iPad many hours a day. There are a few core programs that have become so integral to my workflow, I’m lost without them. One of these programs is Default Folder X. Despite the mysterious name, it has become an essential part of my Mac-based workflows.Default Folder X combines folder navigation, OpenMeta tagging, and host of other features into a single, easy-to-use interface that interdigitates with the built-in Save Dialogue Box.The three features I use most commonly are the Recents Menu, OpenMeta tags, and the Favorites Folders.The Recents Menu keeps track of the places you’ve most recently saved information, allowing single-click access to your most recently saved-to folders.dialogue boxThe OpenMeta Tags box lets you tag files before saving them, sparing you the need to go back and label them at a later time (I’ll cover tagging in a later entry).openmetaI usually work on several concurrent projects. Using the Preference menu of the app, I can designate current project folders as “Favorites.” I can then open these folders through key combinations, greatly speeding up access to the information contained within.preferencesDefault Folder X is another program I use dozens of times each day. You can download a copy and try it yourself for 30 days at St. Clair Software’s website.

Core Software for the Mac: LaunchBar

Over the years, I’ve adopted several pieces of software that have completely altered the way I use my Mac. One of these is LaunchBar. LaunchBar is a "launch application" for Mac OS X, providing access to my applications, folders, and files by merely typing the first few letters of their name. For me, LaunchBar serves multiple purposes: a clipboard manager, an iTunes controller, a search tool, and a calculator all rolled into one. This allows me to access anything on my computer without lifting my fingers from the keyboard. I merely invoke LaunchBar using a key combination (I use Command-Space) and then type in the first few letters of what I want to do. LaunchBar returns the top hits in a small menu at the top of my screen. Out of the box, a Mac will launch Spotlight if you hit Command-Space. You have to turn this feature OFF in the Spotlight Preferences (in System Preferences). Spotlight Preferences You also have to designate the key combination you wish to invoke Launchbar in the Launchbar Preferences. LaunchBar Preferences In order to appreciate the broad range of possibilities with Launchbar, take a look at the Features. Even better, Download the free 30-day demo and work through the short Tutorial. I use Launchbar hundreds of times every day. I am literally lost on my computer without it. I will cover the other core pieces of software in future entries.

Writing Workflows: Processing Annotations (All Roads Lead to Skim)

One of the great things about the internet is its ability to enable collaboration--workflows are never static, each of us builds on the work of others to enhance our own productivity. After my last post, Writing Workflows: Capturing Annotations to Enhance Scientific Writing and Knowledge Retrieval, I received a boat-load of comments, suggestions, and links. Thanks!I suggest you take a look at an entry in Aleh Cherp's excellent Macademic blog. In a recent entry,  a guest author discussed  limitations with the built-in annotation tools of Papers, Sente, and Mendelay. His preference for annotating manuscripts is the open-source Skim. I've been playing with Skim recently (especially some of the post-annotation processing tools). I used Skim in the past, but curtailed my use in order to simplify my workflow (doing everything within Papers2). Despite the rich annotation tools in Skim, I set it aside because of the extra steps needed to make Skim highlights visible in Papers (and visa versa).As pointed out in the comments section of my last entry, the Achilles Heel of my annotation workflow is the need to separate my highlights / notes file by hand (Papers puts out a single aggregate file with all highlights and notes batched together). Although there are scripts available to send Papers2 notes to DevonThink Pro, I could never get them to work properly. I'm experimenting with a modification to my previous workflow--one that will significantly speed up the process:

  • I highlight and make notes in Papers2 on my Mac or iPad as I discussed in my last entry
  • When I've finished annotating, I make sure the most current version of the paper is synchronized back to my Mac. I then "Export PDF File and Media" from the File Menu in Papers2 and save to a convenient location (I use my Desktop). 
  • I then open the document saved to the Desktop in Skim and choose "Convert Notes" from the File Menu in Skim (this results in all the embedded notes being converted to Skim Notes).
  • I open and select the "Inbox" of my Literature Database in Devonthink (this is the location the script will save my comments).
  • With Skim still open, I run the following SKIM PDF Notes to DEVONthink script I downloaded here.
  • I return to my Inbox in Devonthink where I now have individual RTFs for each highlight or note. 
  • I insert my own comments (if I have any) in each RTF file and save each file. I ignore the link the script generates.
  • If I have a comment I plan to cut and paste directly into a future project, I append my comment with the Papers Citation Index.
  • In DevonThink, I highlight then drag and drop all the RTFs (but not the duplicate PDF of the paper) to the "Supplemental" Tab of the manuscript in Papers (this copies each RTF into the Paper folder hierarchy).
  • Finally, in Devonthink, I Index (the first time) or Update the Index (all subsequent times) - NOT IMPORT - the folder. 

The SKIM PDF Notes to DEVONthink script saves me quite a bit of time--I no longer have to parse my comments by hand. Happy writing!

Writing Workflows: Capturing Annotations to Enhance Scientific Writing and Knowledge Retrieval

As I mentioned in a previous post, reading and writing are central to my academic career. I am a voracious reader. I not only have to keep current in my clinical specialty, Anesthesiology, but also in my research areas, Simulation and Games Based Learning. Because of this, I’ve developed multiple workflows that make reading and annotating more enjoyable, efficient, and useful.I’ve mentioned my preference for Papers2 app to keep track of scientific publications. What I didn’t mention is that I’m a prodigious highlighter-it is not uncommon for me to mark up a single manuscript with dozens of highlights and notes. Keeping track of the information in manuscripts AND my thoughts about what I read used to be a real chore. Before Papers included highlighting, I had a complex workflow to accomplish this feat. Now it’s relatively simple.As I mentioned, when working with scientific literature, I like to batch operations. I go on paper collecting binges where I do little (if any) reading. Only after I’ve completed my collecting, is it time to read. I actually schedule time on my calendar to read, annotate, and synthesize ideas.This entry is about my annotation workflow–and how I use technology to speed up the process of retrieving concepts when writing and citing.I do most of my reading (and annotating) on one of two devices: my Mac or my iPad. I read so much, it’s hard to keep track of all the ideas. There are few things more frustrating than knowing I’ve read something, but being unable to find the source. This workflow alleviates the stress of finding relevant information in my library. But even more than that, using artificial intelligence in a tool called Devonthink, I can find links between concepts that were not initially apparent to me.This workflow has been a personal success. Before implementing this workflow, I could spend hours trying to track down an appropriate reference. Since implementing this workflow the same task takes seconds.I also wanted to thank Derek Van Ittersum (Kent State | blog) for inspiring me to polish this workflow–I had a chance to collaborate with Derek on the Mac Power Users 100 show.Programs needed:  

Setting Things Up

I’m assuming you’ve already installed DropBox on both your Mac and you iPad. As I discussed in a previous entry, I configure Papers save PDFs to a designated folder Dropbox. I set this up by navigating to the preference menu in Papers and designated my preferred folder you in Dropbox. I do this to have the PDFs in my Papers collection accessible from anywhere and by any tool.How Papers handles PDFsWithin the Papers preferences, I’ve configured Papers to launch a PDF in a new tab (using Papers itself, NOT an external PDF reader).Launch PDF within Papers

Annotating

Papers on the Mac and iPad have built in highlighting tools (on the Mac, invoked by hitting the control key over highlighted text, or on the iPad by holding a finger down and dragging). As I highlight or make notes in Papers , a separate layer is created in the PDF that keeps track of annotation information. As I annotate, each highlight and note appears under the “Notes” tab in Papers.Notes Tab in PapersIf I find a paper I’d like to read that’s not in my library I copy and paste the title and author to my OmniFocus Inbox-to be gathered during a future collecting binge. This way I don’t interrupt what I’m doing.After I’m done highlighting and note taking, I write a single summary note that captures the essence of the paper. At this point I also tag the paper Papers Keywords. Once I’ve completed my summary, if I’ve been reading on my iPad, I synchronize the PDF back to Papers on my Mac. After syncing, the annotations I made on the iPad are available on the Mac (and visa versa). If I’ve been reading on my Mac, I don’t need to synchronize to perform the next step.Once the annotated PDF is in the Papers collection on my Mac, I go to File:Export:Notes within Papers (make sure the “export selected paper” is highlighted and RTF is selected) to export a Notes file to a folder on my Desktop. RTF format is important–Devonthink relies on it.Export Notes from PapersA limitation of Papers is that it can’t export each note or highlight separately–it dumps all my annotations into a single file. I open the file and cut and paste each individual note (that represents a single highlight) into its own file. I then comment on the highlighted passage. Finally, I use the “Magic Manuscript” feature of Papers (invoked by hitting my Option Key twice) to append the citation reference to each statement.Extracted Note with Magic Manuscript CitationFinally, I drag each RTF into to the “Supplemental Files” tab of the Papers. This saves each comment in a supplemental folder residing side-by-side with the manuscript in the Papers Dropbox hierarchy.Adding RTF to Supplemental Files in PapersThe next step of the workflow uses the “Indexing” feature of Devonthink Pro Office. Using Devonthink, it is possible to index (or reference) any folder on your hard drive. This makes the contents of PDFs and RTFs available to Devonthinks Artificial Intelligence without directly importing the information into a Devonthink Database.I created a Devonthink Literature Database that indexes (does not import) my Papers2 Folder. I did this the first time by opening the File:Index… Menu item in Devonthink and navigating to the Papers Folder in Dropbox. All subsequent updates are done by opening my Literature Database, highlighting the indexed “Papers2” Folder, and navigating to File:Update Indexed Items. Indexing can takes quite some time–be patient.Devonthink IndexingThis all sounds complicated, but trust me, it’s worth it. What this allows me to do is open Devonthink and find any statement, concept, or related item quickly. I can then cherry pick comments related to my search and paste them into a draft document with little modification.When I’m writing, I take all related concepts and paste all of them into a single card in Scrivener. This allows me to arrange, and rearrange information to help support my argument. Because I took the time up front to include the Magic Manuscript Index from Papers, no further searching or citation work is needed, until I’m ready to format my bibliography.Scrivener for iOS is under development–it is likely my workflow will change when it is released. Instead of using Scrivener, one might consider using Tinderbox –Derek’s tool of choice or the newly announced Scapple (by the makers of Scrivener). I will cover the next step of the writing process using these tools in an upcoming entry.

Closing

In this entry I’ve covered my annotation workflow and how I make use of my annotations when writing. Using Dropbox, I can access my highlighted manuscripts from anywhere. Using a combination of Papers and Devonthink I can make use of my annotations saving me countless hours of time when writing.

Scapple - Scrivener's little brother now in beta

I am a frequent reader of David Sparks blog MacSparky. I found a link to a new piece of software by the folks at Literature and Latte (developers of Scrivener). Scrivener is a fantastic piece of software for writing and an essential  tool in my writing productivity arsenal--I'll write about how I use it soon.  Scrivener's new little brother is Scapple--a brainstorming application now in beta. Scapple allows you more flexibility in capturing and organizing your ideas than traditional mind mapping software.You can read about and download the Scapple beta here.

Writing Workflows: Collecting Information in Papers2 (MacPowerUsers Show 100)

I had a great time as a guest on David Sparks and Katie Floyd’s milestone MacPowerUser Show 100 yesterday. Their podcast has been a staple on my iPod and iPhone for years. To celebrate they invited 10 guests to discuss workflows in their professional lives. Over the past several years, I have learned an incredible amount from Katie and David. It was nice to be able to give something back.I had the pleasure of discussing a portion of my writing workflow–how I get information into my academic research library-Papers2. I’ve talked about why I use Papers in a previous entry. If you’re not familiar with Papers you should read my previous post first. Go ahead. I’ll wait.——————————- Okay, welcome back.When tackling a new writing project I pass through several stages:

  1. collecting
  2. organizing
  3. reading
  4. synthesizing
  5. citing

The workflow I covered on the MacPowerUsers had to do with collecting information. I usually obtain scientific literature in one of three ways:

  • as a recipient of an Endnote library (when writing collaboratively)
  • through personal searches on the web
  • as an attachment to a colleague’s email.

I’ll cover each of these contingencies below.Endnote still has quite a foothold in academics. I often find my collaborators have not yet made the switch to Papers. Many times, when writing collaboratively, we must share libraries between the two applications (Endnote and Papers). Fortunately Papers can import (and export) Endnote libraries seamlessly (as long as they’re in Endnote XML format). Easy and no need for a workflow!However, the other two situations are more complex (searching myself or receiving attachments to emails) and require a workflow–making use of the wonderful program called Hazel. Hazel monitors folders on my computer and acts on individual files according to rules I create. Hazel can even peek at the content of files and “recognize” what's inside. I have Hazel monitoring about a dozen folders on my Mac, but my Downloads Folder keeps Hazel the busiest. I have about two dozen rules running on my Downloads Folder alone.For this particular writing workflow I ask Hazel to look at the contents of every PDF in my Downloads Folder and match files that have words unique to scholarly publications.I’ve found having Hazel search for the word “References” within each PDF works the best. When a PDF whose contents contain the word “References” is matched, Hazel automatically launches Papers and imports the manuscript. While importing, Papers fetches metadata, renames the PDF to the convention I’ve specified, and files the manuscript in a specified hierarchy on DropBox–all automatically. Another preference in Papers erases the original file once it’s imported.I’ve tried other search words for Hazel including “abstract,” “methods,” “results,” and “discussion”–none work as well as references. Most every scholarly manuscripts has references (unfortunately, even the word “references” will not be 100% reliable–in a minority of publications, references will be called a "bibliographies" or "citations").You are probably wondering why I don’t just use the built in unified search window in Papers. My answer: it is faster and less frustrating to find full-text directly through our Library’s web page. Papers unified search will work through a fire wall (using proxy URLs in the search interface) – but it’s hit-or-miss whether a link in Papers will lead to a full-text article or merely a frustrating publisher’s login screen–most usually the latter. My hit rate is much higher on the web. I use Papers built-in search engine primarily to retrieve metadata (after the full text pdf has already been imported).When I’m collecting full-text articles I save EVERYTHING to my Downloads Folder and let Hazel do the rest. When she finds a match, she launches Papers and imports each manuscript without any additional effort on my part. Using this method, I can conduct my search for scholarly information with minimal interruptions - Hazel does the rest.Searching on my own is the most common way I get information into papers, but occasionally a colleague will mail me something they think I should read. For these situations here’s what I do. I have Hazel monitor my Mail Downloads folder (~/Library/Containers/com.apple.mail/Data/Library/Mail Downloads ) and copy EVERY attachment to my Downloads Folder (I do this for a host of reasons–not just publications–I’ll talk about why in a future entry) Once the paper is in the Downloads folder Hazel can work her magic using the rule mentioned earlier. Apple now hides the Library Folder by default. Here is a quick tutorial on how to find it on your hard drive (works for Lion or Mountain Lion).So there it is: how I use Hazel to speed up the collection of information when writing or researching. I hope it’s helpful to you. In a future entry I’ll talk about an emerging trend in research paper management: social networking.Cheers, Jeff

Soulver-Budgets and Calculations Made Easy

In my various roles at Duke, I frequently develop budgets. These may be estimates for simulation training exercises, budgets for research proposals, or quick two or three variable calculations.

In the past, I'd build the preliminary budget on a piece of paper, then add each item up using my Mac's built-in Calculator app. If I felt really daring (and had time), I would develop an Excel Spreadsheet-but building the formulas often took more time than I was willing to spend. I longed for something more sophisticated than paper yet less complicated than Excel–then I found Soulver.

Soulver is a program developed by Zac Cohan and Nik Youdale of Sydney, Australia. Soulver let’s you type a free flow of ideas and numbers into a simple interface. The program is smart enough to extract the numbers and operations from your free text and do calculations for you.

I find this program invaluable when developing preliminary budgets for grants–I’m able to jot my ideas down quickly. If I make a mistake, I delete and re-write a line (rather than starting the calculation from scratch). When I’m satisfied, I send the Soulver file (or a PDF) to our Financial Management Coordinators who can develop our “official” budget. I also use Soulver when asked to do a quick cost projection or when jointly developing budgets with others.

The available operations are quite sophisticated and include: symbols, words, percentages, functions, variables, and more. It also understands 90 different currencies.

For $11.99 in the App Store, Soulver is fantastic bargain. If you want to take it for a spin, there is a 10-day free trial from the Acqualia web site.

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.

CheatSheet Instantly Displays All the Keyboard Shortcuts for Mac Apps

I found a story on Lifehacker about an app called CheatSheet. The app sits in the background of your computer, but if invoked (by holding down the Command key) it brings up a list of key combinations that can be used with the program in the foreground.

Learning keyboard shortcuts can improve your productivity significantly.  I tested CheatSheet with several of the programs I use commonly--CheatSheet worked for them all. The utility is free--and worth far more than its price (it's free!).

(Via CheatSheet Instantly Displays All the Keyboard Shortcuts for Mac Apps )

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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