TreeView X now on Google Code

TreeView X, the open source version of TreeView, has been slowly suffering bit rot as C++ compilers and operating systems change. Every so often I'd tweak the code to build on some Linux version or other, but this isn't something I've a lot of time for. Moreover, because of the hassle of rebuilding binaries and source tar balls the updated versions weren't uploaded to the TreeView X web site. Charles Plessy has been doing a nice job of keeping a Debian package working, but my own code wouldn't build on newer versions of Linux.

Today I managed to get my code to build on Fedora Core 13 using gcc 4.4.4 and the latest stable version of wxWidgets (2.8.11). The program runs OK, although there are some display glitches, and printing seems broken. However, my days of standalone application development are over, so I thought I should make the code accessible to anyone else who may find it of use. The code is now hosted on Google Code.

Viewing scientific articles on the iPad: towards a universal article reader

There are a growing number of applications for viewing scientific articles coming out for the iPhone and iPad. I'm toying with extending the experiments described in an earlier post when I took the PLoS iPad app to task for being essentially a PDF page-turner, so I thought I should take a more detailed look at the currently available apps. In particular, I'm interested in how the apps solve some basic tasks, and whether there is a consistent "vocabulary" for interacting with an article. Put less pretentiously, do the apps display things such as lists of articles, citations, references, figures, and bibliographic data in similar ways, or does the user have to learn new rules for each app? I'm also interested in how the apps treat the article (e.g., as a monolithic PDF, as a document with pages, or as a web document where pagination has no meaning), and how they get their content (from a publisher, from the user's social network, from the user's personal library).

Nature
In this post I'm going to look at Nature.com's app. Future posts will explore other apps. I'm interested in what people have done so far, and how we could improve the reading experience. Long term I'm interested in whether there's scope for a "universal article reader" that can take diverse formats (including XML, PDF, and page images) and display them in a consistent and useful way. In the diagrams below I'm using touch gesture symbols from Graffletopia (see Touch Gesture Reference Guide).

Contents
Nature's app is limited to articles published by Nature, and displays the available articles as a list with thumbnails of a figure from the article. The app fetches this list using Nature's mobile API. Up until April 30th the fulltext of an article was free, at at present you are limited to getting abstracts. It's interesting that the list of articles isn't retrieved using a RSS feed, I presume because Nature wanted to use some simple authentication to avoid users downloading all their closed-access content for free.

Article display
Nature's app, unlike all the others I've seen so far, doesn't use PDFs. Instead it uses ePub. Unlike many ePub book readers (including Apple's own iBooks), the Nature app doesn't render the article as a series of pages, but as one continuous document that you scroll down by dragging (it's essentially a web page). You can't zoom the text, but the text size is fine for reading.

Citations
Citations in the body of the article are links. If you tap them the full citation slides in from the right, with a link to the publisher's website. If you tap the link the app opens the website within the app. This can be a little jarring as you move from a customised view of an article to a web page designed for a desktop. In the case of a Nature article, it would be more elegant if the app recognised that the cited reference was a Nature article and rendered it natively in the app. More generally the transition between app and website might be less jarring if journal publishers developed mobile versions of their websites.

Figures
The figures aren't displayed directly in the body of the article, but each mention of a figure in the body of the text is a link. Tapping the link causes the figure to slide up from the bottom of the screen. A button in the top right hand corner enables you to toggle between displaying the figure and it's caption (shown as white text on a black background). You can use pinch and spread to zoom in and out of the figure, as well as save it to the photo library on your device.

Summary
I've started with the Nature app as I think it's the only one so far to seriously tackle the challenge of displaying an article on a mobile device. Instead of displaying PDFs it repackages the articles in ePub format and the result is much more interactive than a PDF.

I hope to explore other article viewing apps in later posts, but it's worth noting that we should also be looking at other apps for ideas. Personally I really like the Guardian's iPhone app, which I use as my main news reader. It has a nice gallery feature to display thumbnails of images (imagine a gallery of an article's figures), and uses tags effectively.

More on the Mendeley API

After playing with the public API for Mendeley over the weekend (see Social citations: using Mendeley API to measure citation readership) I've had a quick play with the user specific part of the API. This API enables apps to connect with a user's account, so you could imagine using it to personalise citations lists (as I mentioned in the previous post), or building apps to handle a user's reading list (to complement Mendeley's existing desktop and iPhone clients).

Once again, it's frustrating just how rough the API is. The documentation is incomplete and contains errors, and some of the API calls simply don't work (see this post). I know I'm sounding like a broken record, but this API really needs a test suite. The quickest way to annoy potential users of the API is to get them to find really obvious bugs for you.

With a test suite in mind, I've created a simple app that enables you to connect to your Mendeley account and perform a bunch of simple tasks. The hardest part of getting this working was getting my head around OAuth. Luckily, @abraham has written a PHP library to support OAuth access to Twitter's API, so I grabbed that and replaced Twitter-specific code with the equivalent code for Mendeley.

Demo
You can try the app here: http://iphylo.org/~rpage/mendeley/moauth/.

The first time you go to the app is shows a button to connect to Mendeley. If you click on it you'll see something like this:

(if you're not already logged in to Mendeley it may ask you to log in — note that all of this happens on Mendeley's site, my app never knows your username or password details). If you're willing to try the app, allow it to connect to your account. You'll then see a bunch of API requests and results. All but one of the requests is simply displaying information. One request does try to add a test document (the one listed on the Mendeley developer's site), but at the moment this part of the API doesn't seem to work (nor does the call to get the list of papers that you've authored).

If and when Mendeley get the API working fully (and documented) there's a lot of scope here. But what I'd really like to see is Mendeley develop a test suite that runs through every API call and checks that the methods work as advertised.