iPad: Reading for Research

A number of iPad software apps support reading, reviewing, editing, archiving, and sharing documents. The increasing popularity of the device among students and faculty raises questions about the usefulness of those in the context of research: How to manage bibliographies? How to store and share annotations? How to access online academic journals?

Together with my colleagues Regina Roberts and Carlos Seligo I recently offered a workshop
where each of us demonstrated one of our most used iPad apps to manage the reading of documents. Here are my notes about GoodReader [1].

1. Reading and Annotating

The main purpose of GoodReader is to serve as reading and annotation tool for pdf files that can be quite large (i.e. in the 100MB range).

The main window when opening a PDF file is intuitively designed with a toolbar for navigation and adjustments of the viewer at the bottom, tabs for all open files at the top, and annotation tools to the right, which are pretty much self explanatory.

When you decide to annotate a pdf for the first time, GoodReader will prompt you with the option to save the annotations to a copy or to the original file. Note that text annotations in GoodReader are not searchable, only the main text of the PDF is (provided it has not been scanned as an image, of course).

Once annotations are saved, there are several options to export those. You can sync with some external drive or device (more about this below), which will copy the pdf file including the annotations to the sync location as-is. You can also email the file. That will give you the option to only email a summary of the annotations, to email the summary and the file as-is, or to “flatten” the file, which incorporates the annotations into the file.

A summary consists of a simple text file, like:

File: johnsonandhalfacre - annotated.pdf

Annotation summary:

--- Page 1 ---

Text (black), Oct 26, 2012 5:39 PM:
This is a note

Arrow (green), Oct 26, 2012 5:39 PM

Drawing (red), Oct 26, 2012 5:39 PM

(report generated by GoodReader)

The reason why this may be useful is that the annotations, while being detached from the original file now have become searchable.

GoodReader also opens a series of other document formats, like html webarchives, ppt, excel, doc, and image formats. It is possible to open and to read docx files. Not all of them opened for me, though, and I am not sure why. However, it is not possible to annotate any of the files of those types.

It is possible to create a stand-alone text document, with no formatting. I have used that feature occasionally to comment on documents, but it editing is a little cumbersome and there is no real integration with a pdf file.

2. GoodReader syncs with…

The upload of articles into GoodReader can happen in various ways. GoodReader, like many apps can sync via iTunes. Articles can be loaded directly from the web (see section below). It is also possible to set up a local webserver, that can be accessed from your laptop.

The option I use most often is the connection to external storage, which allows to easily share a set or subset of readings across devices. These options are accessed through the Connect to Servers Section of the main interface.

Goodreader connects with a series of external services, I use Dropbox, Box, Google Drive and WebDAV. The setup is self explanatory. Once connected, files or entire folders can be copied back and forth. It is also possible to enable automatic syncing of folders.

Stanford IT recently made both 25GB Box and 5GB Google Drive cloud storage accessible as Single Sign On (SSO) with SUNet ID and password.

However, GoodReader does not directly support SSO. If you set up a connection in Goodreader with your Stanford email, it will not accept your Stanford Password as login.

To get around this limitation, Box allows you to set a so called “external password“. Note that this should *NOT* be your SUNet ID password for this! You can set this in the web interface of https://stanford.box.com/. Log in to your account and open the Account Settings. Then use that external password to authenticate to your Stanford Box drive in GoodReader.

Google Drive does not allow you to set such an external password. So my workaround for Google Drive is to download the free iPad app for Google Drive. If you switch and login to the App with the Stanford email and no password, it will redirect you to the familiar Webauth login. You can then open the file and use the “open in..” option to load the document into Goodreader, similarly as one would do from the Web Browser (see below).

I use the WebDAV server connection to access course readings on Coursework. Coursework allows to connect directly to the materials section of a class via WebDAV. Instructions as of how to do this are on the Coursework materials page under the Upload-Download Multiple Materials Tab.

Syncing with mail servers might for some be a convenient way to transfer documents. GoodReader detects emails with attachments and only loads those into the view, allowing to select the ones to be downloaded.

3. Downloading from Jstor (and alike)

As an alternative to shared drives GoodReader has a built-in browser to search for articles. This allows you to access Jstor and similar repositories directly. Once accessed, the article can be downloaded using the download icon at the bottom of the screen. Articles are downloaded into the “Downloads” folder. The built-in browser is rather simple and the interface is unnecessarily complicated, as one is prompted at every link if to follow it or to download it.
So I more often switch to the Safari web browser on the device. Once I have found the article I use the “open in… ” option (Note that Chrome and Google Browsers do not have this option) to download it to GoodReader. The downloaded article ends up in the default top folder called “My Documents”, so I usually move it and rename it.
As a reminder, connecting to Jstor and other restricted resources from an off campus network requires your proxy to be configured. It is also possible to use VPN, VPN in turn requires the iPad to be on a wireless network, a cellular connection will not work.

4. File organization

File management with GoodReader is done through the main interface as well and is mostly self explanatory. However, it is one the critique points for this app, because interaction relies on the more traditional metaphor of “clicking” instead of the more intuitive drag-and-drop. Syncing of entire folders is possible. It allows for nested folders, which makes it easier to organize large numbers of files on the device.

5. GoodReader is not the only one

I originally started out with iAnnotate as pdf reader as it was adopted by the Stanford School of Medicine, but I found it hard to navigate and was overwhelmed by the number of tools that cluttered the interface when reading and a clumsy file management system at that time. So I soon moved to GoodReader – at a time when it still sold for $0.99. I have heard positive comments from my colleagues about iAnnotate lately. The most recent app on the market is PDF Expert. All three of these apps are identical in their core functionality of syncing and annotating, and different in the extras, for example tagging or searchability. iAnnotate appears to be moving towards an account based approach, it is necessary to create an account to take advantage of new features. PFD Expert currently has the highest rating of the three on the iPad store. Here is an extensive, relatively recent review comparing PDF Expert, iAnnotate, and Goodreader.

[1] NOTE:
There is a free app called Goodreader for Good. It is specifically designed for Good for Enterprise users. Good for Enterprise is a $1500 collaboration suite for secure encrypted transmission of files.
In order to be able to use the Goodreader for Good it is necessary to have access to that infrastructure.

GoodReader App on iTunes ($4.99)
GoodReader User Manual

Other PDF Reader apps:
iAnnotate App on iTunes:($9.99)
PDF Expert ($9.99)

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