Mobile Scholar: Part 3

I've thus far written two posts on how to turn my iPad into a computer. I am doing this both because I am too stingy to buy a MacBook Air and too stubborn* to give up.

My number one "killer app" has been the ability to work on papers from anywhere using LaTeX. I am now able to fully do this (provided the iPad has an internet connection). Here are step-by-step instructions for anyone interested in trying:

Step 1: Get Dropbox

This first step is very easy. Dropbox is cloud-based storage that works on every device under the sun, and is really, really fantastic. It's free up to 2 gigabytes, and you get 500 mb for every friend you invite. Unless your papers tend to have gigantic graphs and images, it's likely you'll never come close to that 2GB limit.

Step 2: Start your LaTeX paper on your computer

If you're familiar with LaTeX, this is also straightforward. If you are new to LaTeX, there is a bit of a learning curve but a lot of help out there. In particular, I highly recommend Lyx, which is a cross-platform WYSIWYG editor.

Get everything set up - your bibliography file, tex file, etc. Save it all to your Dropbox folder.

Step 3: Get latexmk going

Latexmk is, by far, the most brilliant piece of software ever written, ever.  If I could write a love letter to its author, John Collins, I would.

What this program does is sit happily in a directory watching for changes to any changes to your tex files... or any associated files (e.g., .bib files)... OR, any other tex files that your main paper references (e.g., chapter1.tex, chapter2.tex).

What does this mean? This means you can have something watching your dropbox folder all day and all night and automatically recompiles your pdf on the fly. Now we're gettin' somewhere.

I believe latexmk is now bundled with all the major TeX distributions. To run it, the magic command you want is:
    % latexmk -pdf -pvc mypaper.tex

Step 4: Get Tex Touch

Tex Touch is a program that lets you edit LaTeX files on your iPad.

I have to tell you, I am not deeply in love with this program because it is extremely clunky for a $9.99 app. (No multitasking support, sometimes crashes, has no syntax highlighting). BUT, it does the one thing no other piece of iOS software does - it understands the LaTeX workflow and syncs to Dropbox. It also sports an easily accessible and well-designed symbol editor so you don't have to go through 18 soft-keyboard screens to find an α.

Step 5 (Maybe?): Get Mendeley

I have Mendeley Lite on my iPad, and while it is also pretty clunky at least it's functional. While writing I can search my bibliography, export a citation in bibtex format (using the web view), plunk it into my .bib file in Tex Touch, and voila. A Mendeley -> DropBox .bib connection would be really nice, and if Mendeley opens up their API maybe I'll write one. In any case, I have high hopes for the Pro version of their iPad software.

That's it! I still would like offline compilation of LaTeX source on the iPad, but I figure by the time someone writes that I'll have bought a MacBook Air. :-)

Happy writing. If you end up trying any of this (or have any suggestions/questions), please drop a comment - I would love to hear how things have worked for you.

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(*) Something that occurred to me recently - possibly one of the best skills you can have as a computer scientist is stubbornness. If you are tenacious and keep trying lots of different things and talking to lots of people until you can get something to work, you will do well in this field. Even if you can't get something to work in the end, just going through the process of trying is a great learning exercise.

Mobile Scholar: Part 2

Awhile ago I promised I'd write about my adventures attempting to turn my iPad into a laptop when traveling. I guess a lot of this is soon moot since Apple just announced the new Macbook Air, which replicates most of the lovely features of the iPad (solid state memory, for instance), but in the meantime what we have is what we have!

For my upcoming trip, the tasks I need to complete are: review several papers, work on a paper due in a few weeks, take notes in meetings, and keep up with the usual barrage of emails. To prepare, I've found a few applications to help make being laptop-less, and at many times network-less, a bit easier.

1. Dropbox for iPad

This is just about the most useful application ever invented. I know, I know, rsync has been around since dinosaurs roamed the earth, but honestly I just never found it usable. I use too many different operating systems and machines and devices that rsync-based solutions were just a nightmare.

Dropbox has been positively a joy to use.  For this trip, on my laptop I downloaded the papers I need to review into my Dropbox folder. Then I synchronized them to my iPad/phone.

Also, most all of my past papers and work-in-progress papers (including my thesis) are stored in Dropbox. I guess this is a bit risky in case they're evil or their servers go down, but it's just a gem when traveling.

2. iAnnotatePDF

From Dropbox, you can send PDF files directly to iAnnotatePDF. I really like to use this application when reviewing papers, because I can put text notes in the margin, circle and highlight things, etc. I mostly use it for commenting on papers written by colleagues and students, but sometimes I use it for conference and journal reviews. 

Its cloud support is a bit weak. Your workflow turns out to be DropBox -> iAnnotatePDF -> [Annotate stuff] -> GoodReader -> Dropbox. 

3. GoodReader

This is the best $.99 you'll ever spend. It strangely claims to be a PDF reader, but really it's a just nice way to access the filesystem, and read/write files to Dropbox, GoogleDocs, WebDAV, and whatever else cloud service you might use. You also can use it as a nice wget/fetch service (e.g., grabbing files off the net and storing them on your iPad). It's indispensable.

Remember my last post about
pseudo-anonymity? I figured
handwriting recognition would
fail if I wrote like a 10 year old.
I'll have you know I am a
Picasso in real life.

4. AudioNote

Honestly, I didn't get this application for the audio recording feature (though that is nice), I got it because you can both take notes with typing as well as sketch with your finger in the same document. I tried about 10 different note taking apps, and this was the only one that handled this feature well. 

5. Instapaper

Every time I see an article I want to read but don't have the time for, I have a little function in all my web browsers, "Save to Instapaper". It pulls down the text (sans advertisements), syncs to a server, and then syncs to all my mobile devices. Then when I'm sitting around in airports I catch up on articles.

I also use Instapaper when I want to save local information about the city I'm traveling to and might not have net, such as train schedules. Sometimes I use Dropbox for that too, but Instapaper is even more convenient because it's a simple one-click process.

6.  RSS

I am still looking for a good RSS reader that syncs with Google Reader. I've just found Mobile RSS which seems pretty decent at first glance. I was using Reeder for awhile, because everyone was singing its praises, but I found it to be too minimal - to the point of being unusable. A few people spoke highly of Byline, but the one time I tried it my finger slipped and I unwittingly did something awful, like, marking several hundred articles as read or unsubscribing to some feeds. I thus deleted the application in a big puff of disgust. 

I'm all ears if anyone has RSS reader suggestions.  

7. Off Maps / OpenStreetMap / OpenMaps

A colleague recommended some open maps apps (heh) to me, and I'll be giving them a shot on this upcoming trip. I'm more inclined to just suffer roaming charges and use Google Maps, but I like the idea of open source maps, and will give it a shot.

8. VLC

This is a jack of all trades video player. It's probably the most useful app I have on my laptop, so I'm thrilled to have it on the iPad. It's great for copying video files to your iPad that you don't feel like converting to some goofy iTunes format (e.g, AVI, XviD, etc). 

9. iSSH

This application is indispensable when traveling. With it I can connect to machines anywhere in the world, easilly get a shell, tunnel stuff, get a nice VNC connection to someplace, etc. Well worth the $10. 

I think that's it. I'm still working on a workable LaTeX solution, which hopefully I'll figure out by the time I write Part 3 in this series.

Sadly blogger is practically unusable from the iPad, so I probably won't be around much for the next week or two.  There are a few blogging apps, but I'm not really ready to shell out for them - I'd rather just google give better support native editing on the iPad. *ahem, evil overlords, ahem*.

Hope you all have a good week and see you soon.

If horses were wishes

Photo by Stuck in Customs

Sometimes I wish I had a cadre of graduate students to help me out with my research. The irony is that in order to prove to future employers that I am able to supervise graduate students, I need to prove that I am capable of "independent research". But the grim reality of independent research in my subfield means sitting in the lab all day and all night alone, toiling away. I do get help along the way, I do "outsource" when I can, but in the end it's up to me to wrap together the whole kit n' caboodle and make the magic happen.

I guess it's different in the biosciences or physics where a whole team of people are working late in the lab on an experiment. But in my field you pretty much fly solo. Even when I collaborate with other researchers, somehow it's still just me writing the bulk of the software, collecting the data, analyzing the results, and writing the paper. (And, apparently, complaining on my blog :))

How collaborative is your work?

Mobile Scholar: Part I

Image by Mike Licht

I am trying to turn my iPad into a laptop in order to lighten my load while traveling (and save my poor neck). It will never replace a proper computer from a software development perspective, but from a scholarly reading and writing perspective I am almost there.

The Chronicle had a nice post in ProfHacker regarding PDF annotation and organization, and Christopher Long has also written in greater detail about how one goes about "Closing the Digital Research Circle". For PDF annotation, syncing, and citing, I strongly suspect Mendeley is going to win the race. As much as I love the idea of Zotero, I just don't use Firefox on any of my machines or mobile devices. (I did enjoy using the open source Aigaion, but once my entire bibliography got trashed while upgrading I decided to stick with the pros). Mendeley can be buggy, but as one person said, "When it works, it works really well," and they're right.

Anyway, that's still just consumption and management of existing content, which is only half the problem. The other is creating and editing manuscripts.

In my field, everyone writes papers in LaTeX. Some journals and conferences occasionally permit the submission of Word documents, but personally I have a hard time understanding how anyone can do that without pulling their hair out. The last time I wrote an article in Word I spent several days dealing with misplaced references, unusual figure formats, caption problems, and incompatibility issues. When I write in LaTeX I can just focus on the writing and ignore everything else. (Kind of like writing a program in Java vs. C++)

But how to write LaTeX on the go? Due to a lack of multitasking in the present OS, as well as Apple forbidding any applications that compile code (e.g., no easy way to typeset your documents), what's a body to do?

I recently found LaTeX Lab, which lets you edit and typeset LaTeX Google Docs. Hooray! Almost there!

...sadly, Google Documents are not yet natively editable on the iPad.

I can, of course, remote login to my machines back at the office using virtualization software and edit LaTeX files there, but that just feels so inelegant. So we're not there just quite yet. I'm going to try a few things over the next few weeks and will report back.