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Clearing the PDF log jam

There is a crisis in medicine, but not the one you think:1

Reading primary literature is superior to press releases and tweets — it sounds so obvious, but not many physicians act on it. There no prizes to be won for not just following the KOLs2, nor do you save any time. Quite the opposite: instead of a promoted tweet about the me-too drug de jour falling into your lap, you need to find a way to identify what’s worth your time reading, and also find time to actually read it — not a small achievement, as highlighted by the above tweets.

But then what? Sure, there is profit at the end of the rainbow in the form of useful knowledge, but merely reading a PDF may not result in any knowledge at all, let alone knowledge you can use. Or, as the underpants gnomes would put it:

Step 1. Read PDFs; Step 2. ???; Step 3. PROFIT!

I too had a backlog of unread PDFs once, spent so much time organizing files and folders, using this and that program to store the metadata3, trying out plain paper, a Kindle, an iPad or two, thinking it is how I was reading them that mattered and oh if only I could find the perfect setting, under the shade of an old oak tree perhaps, with some peace and quiet, a pen in one hand and a cup of coffe in the other, well, then the unread pile would melt away and all would be good in the world.

But reading is easy, if what you read is useful, entertaining, or both. For most people without visual impairments or dyslexia, the log jam is at Step 2. We don’t want to read our pile of PDFs because, in most post-GME circumstances, there isn’t a clear goal to reading them (lest you have superhuman memory).5 This is particularly true early on in your carreer, when you have nothing to hang your hat on mentally, and few connections to make between what you are reading and what you already know. Sure, you don’t need to keep track of the articles you’ve read if the only reason for reading is to pan them on Twitter. You do, however, want to summarize what you’ve read and save it for future use, be it in a lecture, article, grant proposal or a blog post. So if and when you find a fairly obscure but potentially important fact about this or that cellular pathway in a supplemental figure from a CNS-adjacent journal, and you memorize the fact for later use, and then a year or so later you do use it to make a figure for the background section of a clinical trial protocol, well, what you do not want happening in that case is to spend hours of your life trying to retrace your steps and figure out the original source when a fellow asks where you got the data.4

I wouldn’t be admitting to all that if I didn’t think I’ve found a solution. A few years ago, I replaced the unsustainable routine of just-in-time literature reviews for whatever I needed done with a robust knowledge management system — a GTD®6 for ideas, if you will. It got to a point where I can read at least one article every day and skim a few more, get the useful information out and into my app of choice7, and have all the information I need to write an editorial like this in a morning or two.

As with most of the things I do it is too personal and Rube Goldberg-y to be of use to anyone else, but it started with a forum post and a book, and if you’d like to turn your plate full of PDFs into something more usable may I recommend that you start with one or both of those and see how it goes. Could it be any worse than what you’re doing now?


  1. And not only in medicine, of course. 

  2. Key Opinion Leaders, the influencers of medicine before influencer became a real noun. Note that unlike the influencers of social media KOLs don’t use the #sponsored hashtag, though there is a hashtag equivalent

  3. NB: if you write any sort of scholarly texts you will still need a reference manager, no matter what system of organizing PDFs themselves you choose. I recommend Zotero, lest your institution has a requirement for Endnote (which must have quite a salesforce, to so thoroughly insert their buggy, laggy, slob of a program into every academic crevice). 

  4. Yes, this has happened to me. We do have good fellows. 

  5. The clear exception here being board exam and MOC prep, where the goal is obvious and the sources of information are all spelled out. 

  6. © David Allen Co. 2001. It is a good system though 

  7. The app of choice before DEVONthink was Roam, which is a web service and a marvelous one at that, but unfortunately not much into encryption, privacy, and other things people dealing with confidential information like to have in the tools they use. 


How I handle email (which is not how everyone should, but you may find some of these useful)

This is all about work email. I have succeeded in transferring most personal communication to Slack, iMessage, and WhatsApp, with a sprinkling of Skype for the grandparents. The sole holdout is Dad, who insists on emailing me links to Serbian tabloid news, child rearing advice, and recipes.

Inbox Zero is a great idea in its original form: live you life and write your emails in a way that solicits as few return emails to you as possible. It means giving some thought to what you put in your responses, and being clear and definitive about them. It doesn’t mean mindlessly deleting or archiving everything or, even worse, sending out half-baked replies just to pass on the baton when you’ll get a dozen of them in return.

I only check email twice a week day and once on a weekend, and with the explicit intent to clean out the inbox (unless when on service or when I’m the primary attending for a sick inpatient). Never check email “just to see what’s there” unless you have the time and the means to do something about whatever you’ll find. More than once in the past I was left to sour over an unexpected administrative roadblock or a non-urgent patient care calamity during a family event, when I could have just as easily waited for Monday morning.

When scheduling meetings: Doodle (or your preferred equivalent) for more than three people, email is fine for 1 or 2. If using email and I’m scheduling, proposed times, location, and a tentative agenda are all in the initial email. If I’m responding to a meeting request I try to put all of those in my reply, but that also depends on who’s requesting.

I thank in advance, not after the fact, and rarely send emails whose sole purpose is to give thanks.

If I get an unsolicited and unexpected email from someone I don’t know but that’s not obviously a mass posting, I wait for the second one. Most times it never arrives.

If the email looks like it came from a template it gets deleted without being read.

If I am cc’d on an email chain with many recipients and not directly called out, I archive and wait it out. The only exception is when I know that one or two replies from me would be able to end the game of email chicken that these chains tend to become.

The few times that I didn’t follow these guidelines, I came to regret it (confirmation bias warning!). I’m sure plenty of people don’t give it a second thought and go by just fine. But they probably don’t work in health care.

Update: Out of Office messages are equally important, and covered well here. My own recent OoO message was as explicit as it could get without using profanity, and hopefully conveyed the sentiment that no, I won’t be checking messages at all.


Level up

The next time someone asks me about books to read before residency, I will direct them here. You don’t have to be a medical trainee to benefit from these, but that period of anxious anticipation between match day and orientation is perfect for buffing your attributes.

How to read a book, by Mortimer J. Adler

What better way to start learning about learning than by reading a book about reading books?

The Farnam Street blog has a nice outline of the book’s main ideas. The same establishment is now hocking a $200 course on the same topic. It’s probably good, but at $10 the source material is slightly more affordable.

Getting things done, by David Allen

The first few months you will be neck-deep in scut work no matter what you do. After that, though, you will have to juggle patient care, research, didactics, fellowship/career planning, and piles of administrative drek—and that’s just inside the hospital. At the very least, this book will help you make time for laundry (and maybe some reading).

Thinking, fast and slow, by Daniel Kahneman

Superficially, similar knowledge to what is in these 400+ pages can be found in a few Wikipedia entries. But you would miss out on the how and why cognitive biases and heuristics are so important. Medicine and research are bias-driven endeavors, and not understanding them is not knowing real-world medicine.


Only three? Yes. If anything, the two and a half months between mid-March and July 1st won’t be enough to read them all with the attention they deserve. But you should try.


Also, this is happening

Switching to Omnifocus

Or it may happen, eventually, when I get to it. Probably close to the trial expiration date, if ever.

Sigh.


Locked in

Two years ago, I haplessly expressed excitement about my task list manager of choice being updated soon.

It hasn’t yet. Two iterations of iOS and an Apple Watch later, Things 3 is still not available, and I am becoming increasingly annoyed. Inside my mind, two kinds of costs—Ms. Sunken and Mr. Opportunity—are battling it out.

Mr. O has me thinking about time wasted on not being able to turn a next action into a project; or having to make too many taps to edit anything in the iOS app. And then I stress out even more contemplating all the features I don’t even know I’m missing out on—not wanting to find out about those is why I not dare read reviews of the competition.

Ms. S, meanwhile, is raising dread whenever I thinking about moving to Omnifocus, Taskpaper, or whatever the GTD app du jour is—knowing that I would be trading a set of known deficiencies for a potentially grater set of unfamiliar ones.

The mister and missus are irrational beings—even though Things 3 remains vaporware, there have been a few 2.x updates that iOS7-fied the experience—from going flat to adding extensions and notification center widgets. All that considered, I should not spend so much time thinking about an app.

And yet, it is 6pm on January 2, 2016, and instead of writing about getting back to the lab, finally finishing the PhD thesis, or being a haughty gastro-tourist in unseasonably warm New Orleans, I am being much too first-worldly for my Balkano-Serbian comfort.

Which I will add to the pile of absurd reasons for why I dislike Cultured Code.


Shonda Rhimes on work

Work will happen 24 hours a day, 365 days of the year, if you let it. We are all in that place where we are all letting it for some reason, and I don’t know why.

Via Cal Newport’s blog


How to spend a Monday morning train ride

The GTD weekly review does a good of job keeping my task list managable, but not all tasks and projects are equal. It’s good to have a sense of when you might have time for deep thinking versus mindless task processing—-something GTD doesn’t trully account for. I had been doing a variant of weekly planning since high school, until internship destroyed any hope of having a daily, let alone weekly plan. It’s time to start again.

And if you are not following Cal Newport’s blog already, you should. The man is a machine.


Down the vim rabithole

Spending two hours each day on the train, offline and without distractions, gives me an excuse to go down various rabbit holes that a couple of months ago I would’ve thought nothing but time wasters. Starting to read the Dark Tower series—-I’m almost done with the Gunslinger—-is one of them. Re-learning vim—-if dabbling with it in high school 15 years ago counts as having learned it—-is another.

This episode of the Technical Difficulties podcast is what started it, followed by a blog post or two (nay, three) on the perfect setup. Now, I may or may not continue using vim as my primary writting tool—-I would have to figure out how to integrate it into my workflow—-but several things I picked up will always be useful:

  • git is an amazing tool for tracking changes that researchers should use more

  • don’t blindly edit stuff—-dotfiles in this particular case—-on your computer without understanding what those edits mean

  • Solarized should be your default color theme for anything

  • use your macro/keyboard shortcut app of choice (mine is Keyboard Maestro, you can just as easily—-but not as prettily—-use Better Touch Tools) to quickly position windows into quadrants, halves, thirds, etc.

  • there might not be much difference between bash and zsh if you are a beginner, but zsh has the cool customizable prompts

Yes, I am writing this in vim, previewing and exporting in Marked, then posting it manually to Squarespace. The only thing standing between me and a fancy-pants static website engine powering this blog is there being no internet access on MARC trains, and me being too cheap to get a $20-a-month personal hotspot from Spring. That is probably for the best.


Managing photos with Transporter, Hazel, Picturelife, and Backblaze

In the olden days, back when I could keep all my photos on Facebook, photo management was simple. I didn’t have that many to begin with; the ones I did have were grouped around events—birthdays, vacations, etc—and easily organized into albums. I also didn’t care much for privacy, or backups.

Then two things happened: iPhone 4S, and Dora. Every day became a photo-op, with two cameras in our pockets ready to shoot. The DSLR was still there for big trips and Dora’s modeling yet another outrageously expensive dress. This gave us:

  • hundred of new photos and hours of video each month coming from four different sources (our two iPhones, a Nikon DSLR, and friends with their own cameras);
  • no time to sort them;
  • more respect for privacy, but at the same time a need to share baby photos with everyone;
  • panic attacks whenever I thought about having to organize the mess of file names, formats, storage, and backup solutions.

We needed a good method to collect all the photos, organize them for easy access, retrieve them quickly for show-off purposes, and back them up both locally and in the cloud.

Having children usually comes at a point in your life when you care less about money and more about your time—though your progeny will do their best to relinquish you of both. The willpower-depleting effects of a toddler’s tantrum are also well-documented. No surprise then that many of the tools listed below have at some point sponsored a certain Mac-centric podcast that has destroyed many family budgets3. No regrets, though—it all works.

Collecting, with Transporter Sync

For simplicity’s sake, I like systems with multiple inputs to have one central gathering node. Unfortunately, our only desktop computer is a ridiculously noisy four-year-old Windows PC which sits in a usually occupied guest bedroom. The fans that buzz with the sound of a thousand bumblebees instantly disqualify it from a job as a media server, so I had to use my Macbook Pro. Thanks to Transporter Sync, that was easier than I thought possible for an SSD-only machine.

Transporter, similarly to Dropbox, has an iOS app that automatically uploads new photos to a predetermined folder. Unlike Dropbox, there is no monthly subscription—you pay once for the device, and keep using it as long as the hard drive is working. It can also act as a NAS-lite—having access to the folders kept only on the remote hard drive without them occupying the limited space of an SSD, through a Transporter Library folder.

Organizing, with Hazel

A folder full of unsorted cryptically named JPEGs and RAWs is less than useful when your parents want to see all the photos from that trip to Naples back in January.

Enter Hazel, the Swiss army knife of file automation. With the rules I’ve set up, it renames photos based on the date and time taken, tags them according to the device that took them, and moves them to the proper Year/Month subfolder. It does the same with our DSLR’s RAW files, placing them in a separate folder. Since the laptop only has 256 Gb, it moves any files older that three months to Transporter Library, the “special” folder kept only on the external hard drive.

We therefore have the last three months’ worth of photos and videos organized by year and month on the laptop, and our entire collection on the external Transporter hard drive.

Access, with Picturelife

In theory, we could get to all those photos using the Transporter iOS app, but we’re not a masochists. It’s slow, ugly, and not meant for browsing media.

Thank FSM for Picturelife! It sucks up all our new photos and videos from the Transporter—though we’ve excluded RAW files since we do have to pay for all that data2—presents them in a nice web and mobile app interface whenever we want it, and can pass them on to Facebook, Shutterfly, Flickr, or wherever else we choose. It will also, from time to time, send you a “this day in the past” email, with photos taken years ago. When you have as many unprocessed photos as we do, it is a great discovery mechanism.

Did I mention it can send photos to Shutterfly with just a couple of clicks? I still have flashbacks of the last holiday season, progress bar dragging glacially, the upload finishing just in time for me to miss the shipping deadline. Good times.

Backup, with Backblaze and SuperDuper!

Keeping everything on the Transporter and Picturelife as on-site/off-site backups would probably be enough for some. Unfortunately, counting on a VC-backed company that might at any point pull an Everpix to hold all our photos does not seem optimal4.

Which is way Backblaze and SuperDuper! keep copies of all those photos as a part of my general backup system1. If you have a Mac and an extra external hard drive, you should also turn on Time Machine. This way, there are three local copies of all the photos, RAWs, and videos (Transporter, SuperDuper! image, Time Machine), a cloud backup of the same (Backblaze), and an easily-accessible collection of JPGs and videos (Picturelife).

Setting this up is neither cheap nor simple5, but it gives you quick and easy access to all your photos, has several levels of backup, and—most importantly—requires little effort to maintain.


  1. Backblaze will back up the Transporter Library folder, since it doesn’t count as network-attached storage. It doesn’t back up NAS drives. 

  2. We keep RAW files in a separate folder, one that’s not on Picturelife’s monitor list 

  3. Which is why this post has affiliate links. 

  4. That being said, Picturelife is the best of its kind and I strongly recommend it. 

  5. I thought about illustrating it with a diagram of a Rube Goldberg machine. 


Get a journal article through your library proxy quickly with Alfred 2

It is always a pain clicking on a link to a journal article only to hit a paywall. It’s doubly painful when I know I have institutional access via my library’s proxy server, but have to jump through hoops to get it: go to the library website, log in, copy and paste the article name or PMID into its PubMed search box, and finally download the PDF. Arduous, and—turns out—unnecessary.

Enter Alfred 2 workflows. Here’s a nice article I found on Twitter today. The NEJM link in the top right corner leads to an abstract, but I need a special archive subscription for the full PDF. No matter—I can just highlight the PMID and hit my special Alfred 2 keyboard combo:

Since I’m not already logged into the Welch library proxy, I hit a login wall. It’s nothing 1Password can’t solve, but you can also just type in your username and password yourself, like an animal.

And Bam! The ugly but magic button is where it should be. Your institution might have a prettier one.

To make it clear—this simple workflow will do a PubMed search of any selected text anywhere in OS X, all through your institutional proxy server. Finding an interesting reference while reading an article, highlighting its title, and hitting ^⎇⌘P to get to the PDF always feels like magic.

You can download the workflow here.

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