iPad Day 2 -- PDF reading and annotating

One of primary use cases I am testing out on the iPad is reading and annotating PDFs. I am in the process of reviewing 200-300 papers on nanowire/nanotube manipulation via electric fields. Printing them all out would be horrendous and unwieldy – I did print the first 30 and it was a 2 inch stack of paper.

If I could replace 20 inches of paper in my bag with an iPad, that would be awesome. Obviously I need to be able to annotate, extract annotations, etc. Major pluses would be easy downloading from Web of Science searches, and integration with Endnote.

Attempt 1: iAnnotate PDF from AjiDev on the iPad. To make this work, you install a little server app on your Mac/Windows machine and point it at all your PDFs (which you downloaded previously from Web of Science, no integration with, sigh). Then on the iPad, you pull all the papers over (1 at a time, yuck) in the iAnnotate app (the developers say they hope to improve this once they have more time with the iPad). You can then annotate, and upload the annotated papers. Pros: this all actually works, I have done my first 5 papers, I can see living with this. Cons: no integration with Web of Science or EndNote, no integration with Pages on the iPad (that would be killer). And the UI of iAnnotate is incredibly obtuse. Dialogs, toolbars, ribbons, popups, with key commands sprinkled through them all with no rhyme or reason. Figuring out how to upload my annotations took forever (when you have an annotated doc open, hold your finger on the doc name for a while, when you let up a properties dialog will appear, and there is an upload button there).

Attempt 2: Papers by mekentosj. OK this looks so freaking promising but I have been dashed on the rocks. Papers has direct integration with Web of Science and many other paper search tools, and I have tried to set up access. Access is tricky because Web of Science access is limited to subscribing institutions, so you have to go through an institutional proxy, in my case UW. I can configure the logon correctly and see the Web of Science webpage in the app and do searches in the webpage etc. But I can’t get the ezproxy setup right which allows the Papers UI to do searches and downloads. This would be so awesome but I am failing. Apparently if I buy Papers for MacOSX it will automagically sync my collection so that is up next.

UPDATE: OK so I bought Papers for MacOSX and now have tried that. The good news – sync between Mac and iPad is great, much better than iAnnotate. The Mac Papers interface is very nice for organizing PDFs, tagging them, keeping track of read/unread, etc. HOWEVER you don’t seem to be able to markup PDFs in the Mac app or in the iPad. You can add global comments to a paper but no highlighting etc. This is a major downer.