Category: Productivity

How I will write my dissertation

In the spirit of getting my procrastinating done during the holidays (that’s how procrastinating works, right?), I thought I’d share how I choose to write complex papers. For my purposes, “complex” means any paper that involves some combination of:

  • citations linked to some bibliography manager;
  • equations;
  • internal links (a.k.a. “cross references”).

For simpler papers, I really do like Pages. It makes formatting relatively easy, it has (basic) EndNote and MathType support, and it looks lovely on high resolution displays. More recently, I’ve become smitten with Apple’s new Handoff feature that works with iOS 8 and OSX Yosemite devices. Being able to work on a paper at my desk, then pick up where I left off on my iPad as I move to the couch, then switch to my iPhone so I can stretch my legs, is pretty neat. Maybe this will get old someday, but for now it’s the bee’s knees.

Then there are the problems. In addition to the inability of Pages to satisfy my need for numbered equations, Apple is developing a bit of a reputation for poor backward-compatibility. I am terrified by the prospect of trying to open my dissertation in a few years and getting an alert like this (source: Google+):

This is totally unacceptable, and I hope Apple understands what a massive detterent this is.

The opposite end of the usability vs. flexibility spectrum, there’s LaTeX. LaTeX combines the longevity of plain text with a robust bibliography management system, not to mention the fact that LaTeX was conceived for the purpose of printing mathematical formulas. But, as the above links may suggest, LaTeX tools won’t be winning any awards for UI design.

Enter multimarkdown. Developed by Fletcher Penny, MMD allows me to use one of the hundreds of markdown[1] text editors for iOS using a syntax that can be exported as LaTeX. This export process does take some time to set up (see here for details), but once it’s read I simply have to prepend this metadata to the beginning of a file to make it export-ready:

Title: Title of my document
Author: Teddy Svoronos
latex input: /path/to/header/mmd-teddy-header
latex footer: /path/to/footer/mmd-teddy-footer
Base header level: 2
Bibtex: /path/to/bibtex/file/bibfull
Biblio Style:plain

I may get into the details of this setup in a later post; let me know if there’s any interest.

My editor of choice is Byword (which was recently updated to support Handoff), though I use Fletcher’s own MultiMarkdown Composer when I need to get in the weeds of internal links, table creation, and using the app’s native table of contents viewer.

The only potential rub in this setup is if my advisors want to use Word track changes to provide comments. In this case, I’ll have to export my file as rich text and do some manual futzing to make it presentable. Not great, but those occasional costs are outweighed by the benefits outlined above.

Boy, I’d better get writing.

  1. For background on markdown, see Gruber’s original specification. For an introduction to the syntax for non-coders and why you should use it, I recommend David Spark’s excellent iBook.  ↩

Increasingly Irrelevant Distinctions

When I started graduate school a few years ago, I was terribly concerned about my notetaking setup (in retrospect, I should have been more concerned about statistics). I was about to get hammered by information that took a variety of forms: lots of equations and diagrams, but also enough discussion-oriented material to require flexibility in how I took notes. My main candidates, which I used to varying degrees, were:

  • Notes taken on my iPad, a combination of handwritten (with a stylus) and typed[1];
  • Typing notes using MultiMarkdown, to allow for easily formatted text, equations, footnotes, and other wacky content;
  • Going whole hog and taking notes in LaTeX in real time (using TeXpad on Mac or iOS);
  • Handwriting my notes with a pen, in a notebook made of paper. Probably by candlelight or gas lantern.

I ended up with a combination of these, depending on the course and whatever devices I had available. This caused quite a bit of consternation in my workflow-addled brain. What if I needed an equation and couldn’t find it? What if I had different silos of material that adhered to different organizational systems? Won’t somebody please think of the metadata?

Looking back on my 2+ years of notes (which I actually refer to pretty often), I’ve realized how little the input medium mattered. No matter which of the tools I used, everything that I recorded is now either (a) in PDF format in Dropbox, or (b) stashed in Evernote.

Solution (a) should be familiar to you if you’ve made it this far in my post, but it’s worth stressing: keep every bit of digital information that’s important to you in PDF format. It’s standard, it’s viewable on any device, it’s not tied to a large corporation that constantly changes the meaning of file extensions, it’s searchable (especially with solid OCR software on Mac and iOS)…just do it.

Solution (b) is new to me, even though I’ve used Evernote off and on for many years. I’ve only recently started working with Evernote in a way that clicks for me, but I now rely heavily on Evernote’s solid handwriting recognition, which they do automatically once a note is on their servers. These improvements are reliable enough that I can choose to write on my iPad with a stylus and export to Evernote, or handwrite in a notebook and capture it with the Evernote app’s document camera. Here’s an example of some notes I took on my iPad (left) and on paper (right):

Evernote handwriting recognition
Evernote handwriting recognition

As you can see, both notes recognize the word “treat” despite some pretty terrible handwriting.

I’m still working out the kinks of what to keep as a PDF in Dropbox and what to ‘scan’ into Evernote (FYI, Evernote saves these scans as image files). The short answer is that I keep notes that I want to reference in Evernote, and notes that I want to keep working on (including journal articles that I want to highlight) in Dropbox. It’s still a work in progress, but I’m trying my very best not to stress about it. Both are highly searchable, organizable repositories, and Mavericks tags have added the tagging functionality of Evernote to Dropbox.

I’m sure I’ll expound on this in a later post, but hopefully somebody will find this useful.

  1. If you’re interested, I used Noteshelf with a Wacom Bamboo stylus and now use GoodNotes with an Adonit Jot Script. But I digress.  ↩

Wireless Presenting Just Got a Lot Easier

Much has been said about Apple’s updates to Keynote, Pages, and Numbers last year, and much of that has been pretty negative. However, Apple has been rolling out updates to these apps over the past few months and, as of the latest update, has made a wonderful thing possible: it is now easy to wirelessly present and annotate a Keynote presentation with nothing more than an iPad, iPhone, and adapter.

Doing a wireless presentation on the go has been possible, but even the most well-done setups have required purchasing, bringing, and configuring additional devices (MacSparky’s setup, which I have used until now, requires a $99 Apple TV and a $99 Airport Express). Now, I only need three things which I carry around anyway: my iPad mini, my iPhone, and an adapter to hook an iOS device to a projector.

The Setup

The basic setup is to use your iPad as a remote that you carry around, which controls your iPhone that’s connected to the room projector[1]. Here are my steps for setting up a wireless Keynote presentation:

  1. Connect my iPhone to the projector using the adapter
  2. Pair the Keynote apps so that my iPad serves as a remote for my iPhone
  3. Press Play on my iPad
  4. Don’t be nervous and do a really good presentation

I’ll walk you through steps 1–3; you’re on your own for step 4.

Hardware: Connect your iPhone

This is easy. Both the VGA and HDMI adapters also have a power plug, so you can keep your iPhone charged while you project. As for which adapter to purchase, in my experience overhead projectors use VGA, while flatscreens use HDMI. That said, I work in academia, so you private sector folks with the fancy pants might only need HDMI to function.

Software: Pair the Keynote apps

The pairing process can feel a bit tedious, but only needs to be done the first time (your device is remembered for subsequent presentations). Better still, if you’re pairing iOS-to-iOS you don’t even need to be on the same network. Here are the steps:

  1. Make sure Bluetooth is on for both devices
  2. Open Keynote on both devices
  3. On the iPad, tap the remote button on the main screen and tap Continue
  4. On the iPhone, open a presentation
  5. On the iPhone, tap on the wrench icon on the upper right of the screen and navigate to Presentation Tools > Allow Remote Control and turn Enable Remotes on
  6. After taking a few seconds to pair via Bluetooth, your iPad should appear underneath Enable Remotes; tap Link
  7. A passcode should show up on both devices; confirm that they’re the same number by tapping Confirm on your iPhone
  8. Tap Done on your iPhone

Combined, here’s what it looks like on the iPhone:

and on the iPad:

Presenting

I said I couldn’t help you make an awesome presentation, but here’s a neat tip: as of this week’s Keynote updates, you can use your iPad to draw on your existing slides, and draw attention to parts of your slide using a laser pointer function. Here’s what it looks like in practice:

This means that you can walk around the room with iPad in hand, drawing and pointing to your heart’s content, all while projecting onto the room’s projector through your iPhone.

The best part? This is all I need for my new mobile presentation setup:

Enjoy, and please get in touch if you have ideas or suggestions.

  1. In this post, I’m using the iPad as the remote and connecting the iPhone to the projector; this is because I prefer to use the iPad for annotations and reading notes. Feel free to switch the two if you prefer to have the iPhone in hand.  ↩

 

EZ does it

While discussing research workflows with colleagues, I’ve been surprised to hear that many get the full text of a journal article by coming across an article, navigating to their school library website, searching for the journal under E-Resources, clicking on the journal link, digging down to the article of interest, and downloading it.

It doesn’t have to be this way (usually).


In most cases, links to journal pages through your library’s website are identical to their ordinary link + a suffix (called an EZproxy) that validates your school credentials to check if you have access. Thus, instead of:

http://jama.jamanetwork.com/journal.aspx

Your library’s link will look something like:

http://jama.jamanetwork.com.ezp-prod1.hul.harvard.edu/journal.aspx

Your browser can make this change through what’s called a ‘bookmarklet,’ a bookmark that, when clicked, does something with the existing URL in your browser. For my case, creating a bookmark with the following script as its content will redirect a journal’s site through my school library:

javascript:void(location.href='http://ezp-prod1.hul.harvard.edu/login?url='+location.href)

Alternatively, you can simply drag this EZproxy link into your browser bar.

Here’s a list of different schools’ EZproxy URLs. Edit the code above by replacing http://ezp-prod1.hul.harvard.edu/login?url= with your school’s URL.

In practice, this means that if you click this after trying to access a full PDF:

Before

You get this:

After

Now, the caveat: this will not work for certain journals[1]. This may be because your school accesses that journal through some larger database, in which case you may have to go back to your library website, like an animal. But this works for me most of the time; hope you find it useful.

  1. Note that this may simply be because your school doesn’t have access to that journal. Ugh, I know.  ↩