The iPad and PDFs — conclusions for now

Several comments have asked for my recommendations. After two days of tinkering, here is what you should do if you’d like to use your iPad to read and annotate PDFs.

* get the “iAnnotate”:http://itunes.apple.com/app/iannotate-pdf/id363998953?mt=8 app. Its UI needs a lot of work, downloading and uploading are clumsy, but it does a fine job of letting you read PDFs and annotate them, and those annotations are usable back on your Mac/PC.
* install the “iAnnotate PDF service”:http://www.ajidev.com/iannotate/index.html on your Mac or PC. This is a lightweight server that passes PDFs back and forth between your desktop and the iPad. Just point it at the directory where you have your PDFs on your desktop.
* on the iPad now in the iAnnotate app, you can connect to the desktop machine and download PDFs. Unfortunately one at a time. Please Ajidev, add batch transfer capability. UPDATE…hmm batch transfer seems to be happening now. Something I did wrong? Updated app? Either way, awesome.
* Annotate away on the PDF. Personally I use the highlight tool to mark a section, then select the highlight and add a note.
* When done annotating, upload the annotated version back to your PC. This is where the UI really blows. With the doc open in iAnnotate, hold your finger on the doc name in the upper left for a while. You will get no visual feedback. Lift your finger and a properties dialog will appear with an upload option. Upload away.
* Back on your mac/pc, your annotated doc will be in your pdf directory with the words “annotated” appended to the name.

This isn’t bad. It is all very functional. I’ve done 15 papers already and it is becoming natural. How can it be better?

* Integration with Web of Science or other paper sources. The Papers app on the iPad promises to let you download papers directly from WEb of Science and others (tho I can’t make it work with the UW ezproxy settings). This would be very nice.
* Integration with endnote??? I don’t know about this. I use Endnote Web within Web of Science and that works fine, I don’t know what else I need.
* Integration with Pages. Would be awesome to be able to slurp annotations and citations into the Pages app.
* Integration with Papers on the Mac? Don’t know, I’ve just installed Papers, and while I like its organization features, the lack of annotation capabilities makes me wonder if I will ever bother with it.

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.