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.

27 Replies to “iPad Day 2 — PDF reading and annotating”

  1. Please can you write suggestions on how to save a PDF file (from a website) on the iPad? This is as wifi is not every where. Also, how to transfer PDF files to an iPad. I want to buy one and so checking. Thanks.

  2. I do agree completely. If the IPad could be used as a pdf reader by academic people that would be a real app killer. I’m sure there are thousands of people that will immediately run for it. At the moment, though, the real case is pretty depressing: no decent pdf reader/annotation app, no obvious integration with commonly reference manager such as endnote, no seamless integration with other o.s. such as windows.
    The ideal scenario would be an ipad with endnote+evernote+adobe acrobat (or equivalent)
    do you think is it possible to aproximate that in any available combination of sw?

  3. Please keep us updated. I’m a scientist and the same reason why I’ve been waiting for an iPad device for years. I’ve had a kindle DX in the meantime but highlighting and annotations never came to be. I’ve asked for annotations for the mac version of papers but that has never materialized. The first company with easy transfer and annotations will be the savior for academia. I can’t wait to stop wasting trees. What we need is a cross between papers and skim for mac.

  4. Great to hear your impressions. Hope to hear more as this progresses. I’ve been hoping for a while that a slate/tablet will allow PDF reading and markup, including keyword tagging (not just whole documents, but selections of text). It would be great to be able to use the ipad or something like it for notetaking on documents. (I’d really love to use it for taking notes at lectures, too, with a stylus)…

  5. I have been moderately happy the past few days using “Memeo Connect Reader” http://www.google.com/search?q=Memeo+Connect+Reader – it can get docs of various types including PDF from my Google Docs account and store them on the iPad. Plus, it’s got better reading functionality than the built-in Prevew app. But it’s just a reader, no annotation/editing.

    Caveat Emptor – it has been a little crashy, but it launches again quickly. I’m hopeful that now the developers have real hardware to test on they should be able to resolve the crash problems; as an iPhone dev myself I am very sympathetic to any bugs given that only the simulator was available for testing.

  6. Business and technical folks need to read tons of PDF whitepapers, specs, and reports. I’ve been trying a variety of apps on my iPad.

    GoodReader should be called “GREATreader”, but it offers no annotation. It is easy to download PDFs from the web (one at a time), and from server mounts (many at a time) from a Mac or PC.

    Papers is beautiful but largely limited to institution collections (as noted above). I was able to find and download via Google Scholar many valuable documents. BUT while it has a browser, there’s no way to simply enter a URL either to a PDF or a webpage. I find this strange and look forward to an update. But it’s certainly not worth $15 for non-scientific/academics like me as it stands. Sad, as the indexing feature alone would make this a bargain. Once you have dozens (hundreds?) of PDFs, many not well named, and from many sources, including work-in-progress, search and categorization becomes a necessary feature to even find relevant documents. If they de-couple this app from its academic roots it would fly off the shelves.

    iAnnotate PDF is very impressive for its annotation capabilities (but as someone mentioned, the UI is a little crazy). Problem is, I haven’t been able to connect on my Windows machine (testing the Mac tonight). They say they are working on other methods to load PDFs into it. If they can achieve direct web downloads, email attachments and similar uploads…that would rock!

    I’m still looking, and have to remind myself that it’s been less than a week since the iPad appeared. I will be patient…

  7. i have no problems with iannotate working on the mac to serve up docs to the ipad. if you have a problem drop me a note and i’ll help you debug.

  8. The aji reader service works ok on windows BUT the iannotate does not like large docs. Please keep the comments coming. Finding a solution to this issue is important.

  9. I bought the ipad + iannotate for the same reasons most of you outlined here (reading and annotating pdfs for academic reasons). However most of my stuff is already on my windows pc. I tried the aji reader service and the ad hoc connection to get files from my computer, but it doesn’t work. The ipad doesn’t see any server. Come on! we just need a way to work on our pdfs. This is simply ridiculous! what’s the purpose of the ipad and of an app like aji iannotate if I cannot download my pdfs? what do they think we should annotate? and why the app doesn’t see the servers on my laptop?

  10. I like the discussion above. I do believe that annotation of pdf and even note-taking using stylus will come soon. I mean how hard can it be? The huge market demand for those things will bring along attentions from developers soon enough. Also it’s not something impossible to accomplish in terms of hardware. Stylus pen for capacitive screen is nothing novel.

    I’d love to see the day that I can sit in the lounge filled with sunshine in my department, with an ipad in my hand, taking note and reading pdf and actually being productive in a regular work day. That’s right, being able to read pdf and take notes with a device like ipad is essential for any measurable research productivity!

  11. Main objective for my iPad is carrying pdfs without the paper, annotate them anywhere, in the train mainly, and get the annotated pdfs out to my colleagues and students. So iannotate appeared the fist app to buy. This was only to discover that once done, the ipad app has no way to get the pdf out again, nor upload or mail it. It only says “mailing of documents and annotations will be included in version 1.1. So I’ve lost my time annotating the first series of pdf in the airplane. Please aji take this serious, tell us how to get the annotations off our ipads again! This is the reason to buy the device in the first place!

  12. Does anyone know of a website or blog to follow which is devoted to this kind of use of the ipad for academics?

  13. @Brett For reading and annotating papers on the mac it is easy to set up Papers to open pdfs using Skim. Then you can nicely annotate everything.

    I wish there was an iPad version of skim, but the developer has stated that this is not possible due to technical limitations. Perhaps I will look into iAnnotate (now “Aji Annotate PDF” I believe) for the ipad, but I’d rather not lose the hundreds of pdfs I’ve already annotated with Skim.

  14. PDF format is useless in the new digital era because it is fixed-layout format created for printing, not for reading. The sooner PDF dies the better. I use Calibre or http://iiiconverter.com to convert PDF files to ePub format. The result is not always perfect, but overall ePub is the way to go.

  15. Just a heads up, iAnnotate has been updated and it is vastly improved with respect to getting PDFs on and off the iPad. You can now e-mail out or in and do a web search. Tool bars still take some getting used to but hopefully they will improve that with more user comments and testing.

  16. Sh — PDF may be a dinosaur but is still the published format for millions of technical papers and that doesn’t seem to be changing fast. While I agree it is a painful format for online use, it is going to be around for a long time.

  17. I am a PC user, and annotate all my journal articles using Adobe acrobat professional on my desktop. It works great for this. I was hoping that my new iPad would live up to the hype and allow me to continue doing this. Sadly, and as verified by this discussion, the apps are way behind in functionality. For now, the iPad is a nice and expensive toy, but of hardly much use for my work. Alas.

  18. iannotate continues to be supremely disappointing. You can bring files in easily enough from drop box or from email, and you can quite beautifully annotate them in Iannotate. However–and this is the kicker–once you’ve annotated them and email the back to yourself the annotations have disappeared!

  19. Hmm that does suck Fred. Just duplicated myself, that is pretty annoying. I hadn’t tried this til now because i have been uploading annotations using the mac aji reader service which works fine, but a bummer that email doesn’t work.

  20. Has anyone else had the weird issue of downloading PDF from the iPad email. I use to be able to open directly from the email into GoodReader. Working like a charm until last Friday and now all that downloads is a view of the first page. I was hoping to avoid having to lug my laptop w/ me when I travel in order to upload documents. I haven’t changed any settings and I’ve tried emailing from different providers, but it seems to be how the iPad now views PDFs in the email.

    Help/advice would be greatly appreciated.

  21. Staci- I’m having a similar issue. I used to be able to have the option to open PDFs in QuickOffice. but now it defaults to only being able to open in iBooks. I haven’t changed any settings.
    Very frustrating.
    On another note, I’m trying to get PDFs off of my iPad onto my laptop…this would be hugely beneficial as I travel quite a bit and don’t have an air card for my laptop. When im not near wifi, it would be great to use the ipad to get documents from email/web and copying them to my laptop.

  22. Hi Nick, I haven’t had anything open in iBooks except for the items I’ve purchased. I have been able to download items to my laptop from GoodReader. The pdf docs show up in the app tab in my itunes (scroll down past the screens of the iPad/iPhone) and gives me the choice to save when I click on the item I want to download. It’s my favorite app to read scripts and manuscripts for work.

    I’m hoping the changes to the email debacle correct themselves or I will lose 75% of the reason I bought this iPad.

  23. Found the solution for me! It was suggested that I delete Stanza app and my documents would open normally and it does! Even older emails that wouldn’t open before, work perfectly now. But just like Nick, I’ll now be able to open them in iBooks also if I want. An interesting turn of events, but if I can open it in any functioning app, I’m thrilled.

  24. I have been testing Noterize, and it seems very good. It has several ways to connect, including cloud (dropbox, etc.).
    It can annotate any kind of documents, including PDFs containing only bitmap info (such as a scan that hasn’t been run through OCR.

  25. Second on noterize. Everything you can do to paper plus voice notes plus cloud. ONLY weakness is organizing PDFs and you have good reader for that, or readdledocs if you like batch imports and shiny UI.

    Reiterate: noterizenoterizenoterize.

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