Friday, October 07, 2011

Mendeley, Sente, or Papers? No, Zotero and iAnnotate will do.

This is a nerdy blog post, relevant only for researchers.

Every researcher needs to read academic papers. I often do this while commuting or being away from office. It often happens that I don't have a hard copy of the paper that I want to read while being away from office. I never know which paper I want to read in advance.

With the advent of iPad, this problem can be solved by storing all the academic papers in iPad. But that's not the end of the solution. Two more things need to be solved: annotation and bibliography management.

I often highlight some sentences in an academic paper. I also often add a note to the paper. I even sometimes draw a simple graph on the paper. This needs to be done on the iPad screen.

Plus, I need to manage bibliography. Currently, I'm using Zotero for bibliography management, but this Firefox plugin doesn't allow me to read a PDF file with the annotation function. Ideally, every time I download a PDF copy of an academic paper onto iPad, a new entry should automatically be created in this bibliography. Then it's going to be easy to create the section of references in my own paper, in my lecture syllabus, or in an email message that I write to refer my colleagues to the papers they might be interested in.

It seems there is no perfect solution for all these. Partial solutions are provided by Sente, Papers, Mendeley, and iAnnotate.

If I don't need to use an iPad (which is totally out of question but...), Mendeley is the best solution because you can automatically sync with Zotero, which is still the best solution to easily create bibliography while downloading a PDF file of the paper. After visiting the webpage of an academic paper in Firefox, click the reference icon that shows up on the address bar of the Firefox, and then bibliography information will be stored to Zotero and thus to Mendeley. Then download a PDF file from the same webpage to a folder on my desktop computer and drag the icon to Mendeley window. This allows me to read the PDF file on Mendeley, which allows me to annotate.

The problem with Mendeley is that its iPad application does not allow you to annotate. How stupid it is.

Annotation on iPad is not a problem with Sente or Papers. But both are rather poorly designed in terms of the automatic bibliography entry creation while downloading a PDF file of the academic paper. Plus, Sente's annotation function is stupid in the sense that you cannot associate your note to a particular sentence that's highlighted. Notes are only associated with a page.

In terms of annotation on iPad, iAnnotate seems to be the best application. However, it doesn't come with the bibliographic management function. An ideal solution is to combine iAnnotate with Mendeley, but Mendeley does not allow you to read the PDF file annotated with iAnnotate.

What makes things worse is that any of these iPad applications (Sente, Papers, and iAnnotate) is not free. There's even no trial version. Each costs less than 10 US dollars, but should I buy all of these to test which is the best among available?

It seems that's the way to go in the world of Apps. Buy several alternative applications for your iPad (or iPhone) and choose the best....

It seems the quick solution is to use Zotero for bibliography management and iAnnotate for annotation on iPad (with Dropbox used for transferring PDF files from the desktop computer to iPad).

Zotero is very powerful. When you log on to a webpage of an journal article, the address bar shows an icon which can be clicked to create a new entry in the bibliography AND to associate this entry with the link to a PDF file on the web. Clicking this PDF link allows me to save a PDF copy. Since I don't use Firefox for any other purposes (Google Chrome is much better to surf the net), I can set a Dropbox folder for PDF copies of academic papers as the default download folder.

Then on iPad, launch iAnnotate, click the download button on the top-left corner (which shows the list of folders in my Dropbox), then click the PDF copy folder. This updates the list of PDF files in iPad. You need a WiFi for syncing PDF files between the desktop computer and the iPad, but in my office there is an eduroam wireless network. So there's no problem.

So, after reaching a webpage of an journal article, I only need to click four times (twice on the desktop and twice on iPad). Then I'm able to read a PDF copy on iPad. This is very efficient.