How to use iPad if you are a researcher in conjunction with endnote

Discussion in 'iPad' started by Germwise, Jun 5, 2010.

  1. Germwise macrumors regular

    May 2, 2009
    For those of you who are in academia or for whatever reason need to read, review, annotate and organize papers tied to proper citations here is what I discovered is the best way so far.

    Before I figured out the best way for me I downloaded Goodreader, iAnnotate, and Papers.

    While each program had its strengths, the most important feature in my work was annotation as I wanted to be able to keep notes and scribbles tied to their respective papers. In short I wanted to replace the stacks of paper that invariably get lost with a searchable, digital library.

    For this I decided to start a new endnote library in a folder I called thesis. I then added papers on my computer as I saw fit.

    I then installed that Aji (sp?) sync program for iAnnotate on my mac and told it to share the endnote library PDF folder.

    On my ipad, with Aji running on my macbook, I was able to access my macbook server, download each of the pdfs and view them in turn. When I was done annotating them, I simply uploaded them back to the server and they replaced the non-annotated originals.

    Now when I go to endnote and search for a publication, I can pull up the annotated file I had on my ipad.

    There are limitations to this method of doing things.

    First of all, downloaded new papers into the ipad can be complicated as then I will need to upload it to a fresh folder on the mac, then create a new citation and tie it to the particular file.

    Also, there is no internet sync and when on the same wifi, you MUST have the Aji program running. This is a bummer because there is no wifi at work so i'll have to wait until I get home to sync.

    Finally I wish I could search by citation while on my ipad rather than by folders. This is something that papers does, but again papers doesn't do annotation as far as I know and I'm hesitant to buy another piece of software to sync with my macbook.

    Hope this helped and Please let me know if you guys have found a better/different way! I'm looking to streamline this process.

  2. natecannon, Feb 17, 2011
    Last edited: Mar 7, 2011

    natecannon macrumors newbie

    Feb 17, 2011
    Boston, MA

    I'm currently a PhD student, and the iPad has been an awesome tool over the last 9 months or so that I've been using it. It took me a fair amount of research (its what I'm good at!) before arriving at a workflow that I'm pretty happy with.

    I too have downloaded all of the different PDF annotating programs (Goodreader, Readdle, iAnnotate, etc) and have spent time using each one. In my opinion, Goodreader is hands down the leader in this area, especially with its most recent release (3.3) that has made syncing dramatically easier. I used iAnnotate for a few months, but the non-Apple UI and a few other quirks always rubbed me the wrong way.

    Simply hook up Goodreader to your Dropbox account (you do have one right? If not, click here right now!)), and enjoy relatively painless syncing with any Dropbox folder that you specify. Its not technically automatic, since you do have to hit the 'Sync' button, but much easier than dealing with every individual file.
  3. Pyxus macrumors newbie

    Dec 30, 2010
    I am using Sente 6. Libraries between Mac and iPad are synchronized 'over the air' and I can annotate PDFs directly in Sente on the iPad. Annotations are also synchronized automatically with the Mac...great solution so far!
  4. maflynn Moderator


    Staff Member

    May 3, 2009
    This is what I use, as in my job, I need to be accessing PDFs for upgrades and found goodreader to be an excellent tool to help me.
  5. evilgreg macrumors regular


    Aug 13, 2007
    For you people who are using GoodReader, how are you viewing your annotations and markups on the Mac? on OS X doesn't work with the GoodReader markups that I've been doing (highlights, notes, drawing).
  6. akuma13 macrumors 6502a


    Jan 10, 2006

    I would guess Adobe Acrobat Reader would work.
  7. natecannon macrumors newbie

    Feb 17, 2011
    Boston, MA
    Goodreader plus Preview

    This should be working without a hitch for you. Every annotation I make in GoodReader (highlights, notes, drawing, typewriter, etc) shows up just fine for me in Apple's default Preview application. I have confirmed this behavior with a number of my iPad using friends as well. Are you sure you are viewing the correct file saved and transferred from your iPad? The first time you make an annotation in GoodReader, it will ask you if you want to create a new file or save the changes to the existing file. I usually save the annotations to the existing file, automatically sync using Dropbox (you are using this, right?!?), and then when I return to my computer, the file opens in Preview with all of the annotations showing. It's a slick, relatively painless workflow that I have learned to love.

    As a side note, the reverse behavior also works quite well. Any annotations made using Preview (just click the Annotate button in the toolbar to get started with this) show up just fine in GoodReader as well.
  8. natecannon macrumors newbie

    Feb 17, 2011
    Boston, MA
    I currently use EndNote for Mac for all of my reference management needs (the Cite While You Write feature is killer), but the EndNote folks have apparently ignored my numerous pleas for some kind of iPad integration. Supposedly they're working on something, but I've been sending them emails since day one of the original iPad and they've apparently been asleep at the wheel.

    Anyway, so I've been tempted by what I've seen/heard about Sente 6. The seamless integration with the iPad, including annotations, looks really cool, but I've read that any annotations made using Sente on the iPad aren't baked in to the actual PDF, meaning that they won't show up when you view the PDF on your Mac using Preview. If so, that's definitely a deal killer for me.
  9. shhy macrumors newbie

    Feb 13, 2009

    I'm VERY interested in the original poster's Endnote solution and appreciate the posting! I don't know if any of the other posters are interested in Endnote per se... but the comments on the different programs are so helpful. I'm a postdoc, and just got my first iPad. Get ready for a huge head slap -- it just occurred to me that reading PDFs on this thing would be nice *slap*
    I have been completely focusing on the fun side of the iPad, as I had convinced myself long ago that an iPad would never be a serious work tool. Perhaps I was a bit premature...
    Anyway, I have been using Endnote for years, and have probably thousands of PDFs already attached to references in Endnote, and would LOVE to be able to edit those directly. BTW, if you aren't using Endnote to catalogue your PDFs, you have GOT to check that out. Any other ideas on using Endnote on this iPad?
  10. HasanDaddy macrumors 6502a

    Jul 16, 2002
    Los Angeles
    This is a great thread!

    Thanks for bringing this topic up
  11. thibaulthalpern macrumors regular

    May 2, 2008
    East Coast, USA
    I have a love-hate relationship with EndNote. Thompson Reuters, the makers or EndNote, has always overcharged upgrade prices for EndNote, especially when taking into account that one version of EndNote to the next has never been that enormous of an upgrade. Worst of all, in my opinion, is that EndNote still cannot do citations in the footnote properly without the user using tricks like hiding text in order to hid unwanted format which EndNote can take care of if the citation is in the main body of the text but not when it is in the footnote section of an MS Word document. And what, we're up to EndNote x4 now and this problem still hasn't been fully solved?

    Thompson Reuters have never been all that responsive to EndNote users anyway.

    What I do like about EndNote is how it is a good tool to organise citations and PDFs. But, some of their CWYW feature for MS Word still needs work!
  12. porcupine8 macrumors 6502a

    Mar 2, 2011
    Papers on iPad does have some limited annotation - highlighting and the insertion of post-it style notes. No freehand annotation if you just want to scribble in the margins, though. I only just got it and got it synced, so I haven't had a chance to use it much, but I don't do much annotation beyond highlighting anyhow so I doubt it's a problem for me.

    The main problem I have with Papers is the lack of matching on the iPad. So if I find an article while on the iPad, I have to either enter all its data by hand or wait til I sync and do it all there.
  13. Roger Pierce macrumors newbie

    Apr 16, 2011
    Endnote on Ipad

    Having a portable digital library with synced annotations was very important for my research work. I have been using a method similar to notecannon and it works pretty well for me. The Endnote Library folder in my dropbox account (upto 16 GB free if you refer your friends and have a .edu email) which includes the endnote file and the pdf folder is synced to my work and home computers. Any changes/additions to the library is synced to both computers via dropbox.

    For ipad sync, I use goodreader and use the option to sync the dropbox library folder to my Ipad - it is quick and painless to sync everytime with the dropbox endnote library on the web. Annotations made to the pdf either at work, home or on the Ipad also get synced to each other - this works for pdf ebooks as well.

    The only thing missing for me is a way to open the endnote file itself to search for references on the Ipad (useful when you have thousands of references) - and I do not want to use another application just for that purpose, since I need everything to be synced to my desktop endnote library. Thomson Reuters has been procrastinating for almost a year in bringing out an Ipad version. One workaround that I use now is to sync to Endnote web (limited to 10,000 references for now) and use safari on Ipad to find the correct reference and then open goodreader to read the pdf.
  14. zigidabee macrumors newbie

    May 3, 2011
    New at this....requesting your advice

    Folks, I...need your help.

    I've been a PC user all my life, recently purchasing an iPad and downloading both Papers and Pages to use for my EdD (which I've just started).

    I THOUGHT that these things were going to raise my reading of journal article pdfs and writing up of papers to a new level. However, just today, after finally completing the setting up all my pdfs i.e. article titles, journal titles, authors, dates, pages, etc in Papers, I've discovered that all I can do with these pdfs is simply highlight text and make notes. Can't any word processor do this? Then, why is Papers so special??

    What I THOUGHT I could do with Papers and Pages was something like the following:

    1. read pdfs, highlight text, make notes;
    2. view/export/print highlighted text and notes at will (with links to references);
    3. write up a paper, calling up at will any terms/notes/references that are relevant to the concept being discussed;
    4. have Papers or Pages insert the citation in the sentence I am writing in my paper for whatever quote/term/note I wish to refer to;
    5. have Papers or Pages continuously 'build' and revise a bibliography as I continue to write up my paper and citations are inserted into my paper.

    It is the year 2011 and I assumed that all the above was all possible in ONE application. I learned after purchasing the iPad that this was not possible - that I would need at least Papers AND Pages to do the above. Now, it appears from your thread that even these two apps combined cannot do the job I need them to do.

    Can any of you help? What do I need to purchase/download to be able to do the above?

    Finally, I am obviously so new at this that I can't even think of questions to ask BEYOND the above i.e. I'm sure that there are many more wonderful things that the current techology can do for me when researching i.e. cross-referencing, etc. So, if you can help point me in the direction as to what else I can be doing while reading my pdfs to further improve the writing up of a paper, please do so.

    Sorry for the long addition to this thread - your assistance is greatly appreciated!
  15. Germwise thread starter macrumors regular

    May 2, 2009
    I used papers for a while and I was not impressed.

    I never fully made it part of my work flow but my impression was that it was an itunes for pdfs. This is great for a PC but totally unnecessary for a mac that has spotlight search.

    Again, here is my workflow that might help you.

    I use endnote to download my papers, it organizes them in folders if I choose, it keeps the download link, and the pdf file accessible and is fully searchable.

    I sync the pdfs to my ipad where I read them on iAnnotate. I can highlight, make notes on teh side etc. At the end of reading every pdf, I write up a short 2-3 sentence summary on the paper as a note right at the beginning top margin. I copy this short description to the "description" section of iannotate and once more to the EndNote notes section.

    Sync everything again and all notes are baked into the pdf.

    If I want to look up a pdf by words or my notes I use spotlight (not sure if endnote searches based on pdf annotations).

    I can also do the search on my ipad based on my description or title. Finally, endnote has them all organized by tittle and authors etc so you can search that way. I can open it and read my description and notes without having to read the entire paper again.

    For writing scientific papers, I use microsoft word, and I can use the cite while you write on endnote that allows me to add citations based on my pdfs directly to word. It automatically updates the references and will even give you the correct format for different journals.

    Its not perfect, but its the best i've found. Other people swear by other methods since it allows them to better write equations etc. Since I am a biologist, this is what works best for me.

    I'm currently considering switching to honeycomb. I'm seeing how I can workout a similar workflow.

    Also, I recently gave away my ipad to another family member. I'm not sure if I can justify 500 bucks for another one just to read papers. Its definitely more comfortable to pull the screen closer to read a pdf, and you are saving paper. however, 500 bucks is 500 bucks.

    I didn't use the ipad for much other than reading papers and maybe some surfing.
  16. swedefish, May 3, 2011
    Last edited: May 3, 2011

    swedefish macrumors 6502

    Feb 12, 2008
    This exactly how I work. However, I don't really use the annotation feature because it takes too long to type on the iPad. I highlight and use the typewriter feature. Then I open in preview and type out annotations based on my markup. (saves a lot of time). Goodreader is the best app I've downloaded!
  17. zigidabee macrumors newbie

    May 3, 2011
    Thanks, folks!

    Germwise and swedefish, so many thanks for your assistance! VERY HELPFUL. This is all starting to 'sink in' a little.

    Swedefish, I purchased Iannotate yesterday to give it a try after reading Germwise's suggestion, and will have a look at Goodreader next. However, I'll stick with Iannotate for a few days to see how it goes.

    Germwise, I can't find a way (like I was able to do on Papers) to enter a journal article's information for a pdf i.e. Journal's name, volume and issue; author(s), date, etc. Could you share how you do this? Secondly, if I understand correctly, I should have Endnote on my laptop (synced with my Iannotate pdfs) so that when I write up papers in Word, I can 'cite' while I write, yes? I was hoping to have a bibliography automatically generated and maintained/updated as I write up a paper. (Sorry, I'm just trying to get my head around all this.)
  18. xraydoc, May 5, 2011
    Last edited: May 5, 2011

    xraydoc macrumors demi-god


    Oct 9, 2005
    EndNote will do much of this for you (your items 1-5), though it only integrates well with Microsoft Word. Apple's Pages has no API to allow EndNote to hook in to it though you can manually insert reference pointers in to Pages then have it build a bibliography after you're done, but it requires exporting your document as an RTF then re-importing in to Pages. No native Pages file format support (not at least in my somewhat older version of EndNote).

    Problem with EndNote is that there's no iPad integration. I've been asking them for iOS integration since the iPhone's app store first opened in 2008. They'd rather charge you $100 at each new "version" for the most minor of feature additions than spend any money on R&D of an iOS (or Android) app.

    Edit: I re-read your post and I think you're refering to Pages on the iPad and not on the Mac. Pages for the iPad is very, very basic and has no functionality to allow it to create bibliographies on the fly. Not even in conjunction with another app. But even though Pages for the iPad is so basic, there's nothing better on any other tablet platform (Android's offerings are even worse). So if writing and inserting references is what you really need to do, I suggest a MacBook Air or a Windows netbook instead.

    It may be 2011 but we're not quite there yet in terms of doing this on a tablet (though IMHO it's clearly a software/marketing roadblock and not a hardware power roadblock).

    Oh, and a word processor (Pages, Word, OpenOffice, etc.) isn't used to annotate PDF files. But an app like Adobe Acrobat (Windows/MacOS), Apple's Preview for MacOS X and several available iPad apps can annotate PDF files quite well.
  19. thibaulthalpern macrumors regular

    May 2, 2008
    East Coast, USA
    Instead of iAnnotate, I went with PDF Expert. Thus far, the programme is okay. I have sent int a lot of feature requests to the developer and hope to hear back soon. I do like its clean and Apple-like UI interface. My major concern with iAnnotate is the complaints that people have about its UI.

    I have been having trouble uploading a 150MB file to PDF Expert via its Wifi drive method. Hopefully the developer will be able to resolve this issue.

    By the way, I'm also a doctoral candidate in the last writing stages and my main use for PDF Expert is to open and annotate large documents (often they're books in PDF format).
  20. xraydoc macrumors demi-god


    Oct 9, 2005
    There's a review of Papers 2 up on Ars Technica currently. I wasn't aware it was out. Looks as if it can replace EndNote as a bibliography-creation tool within both Microsoft Word as well as Apple's Pages (Mac, not iPad, version).
  21. zigidabee macrumors newbie

    May 3, 2011
    Using iannotate seems to going well so far...

    Thanks for the additional guidance and suggestions, xraydoc and thibaulthalpern, and thanks again germwise and swedefish.

    Xraydoc, thank you very much for taking the time to make my learning curve less steep - your explanations were presented at just the right level for me (although I'm going to be a good student and go look up things like API, reference pointers, etc. in order to understand this all even better). Yes, you are correct, I meant Pages on the iPad. I do think, however, that I will be purchasing a Macbook Pro soon, though.

    I've been using iannotate for a few days now (thanks, Germwise!), and, from a newbie's point of view, it is heaps better than Papers1. I think I'll stick with iannotate for a while now until I get to know it very well, after which I'll be in a better position to judge others.

    Although there wasn't any way (as far as i know) to view all my annotations, etc WITHIN iannotate (please tell me how to do this if it CAN be done), when I sent an annotated pdf to iBooks, for example, I saw all of my annotations on the last page. :)

    NOW all I need to do is to learn how to 'sync' (as Germwise stated) iannotate to endnote on my laptop. What does 'sync' mean, and how does one do this? (I downloaded a free trial version of endnote to my PC laptop a few days ago).

    Once I learn how to do this, I will try the final step: attempt to 'cite while I write' in Word. (I am assuming this is done while having endnote and Word open at the same time on my laptop??

    Wishing you all continued success with your research and/or doctoral papers! :)
  22. Germwise thread starter macrumors regular

    May 2, 2009
    Sorry for the delay in getting back to you zigidabee.

    1) As far as naming each file. I make sure to download the papers to my computer first via endnote. In this way, the naming is done by endnote. Otherwise you may find yourself with lots of file name 28989032.pdf

    Also, when I search for a paper on my ipad, it searches the titles within the PDF.

    2) In order to sync here is what I do. If you visit the iAnnotate website, you will see Aji sync program. You install it on your mac/pc and tell it which folder you would like to sync. Endnote downloads all papers to a particular folder, so I point Aji to that folder. In this way, any new downloaded papers on my computer, appear in my ipad and when I annotate, those PDFs automatically update the "virgin" pdfs on my computer.

    3) As far as viewing all your annotations, there is an option in iannotate to give you a summary of all your notes in the description. Since I wrote the original post I gave away my ipad to my aging grandmother and have yet to buy another so I have no way of finding the exact option.

    4)Finally, cite while you write is easy. Open up endnote, make sure you visit the cwyw options. Write your text on word and when you want to insert, go to endnote and press the insert citation button.

    i'll check out papers 2. I agree that endnote screws with us making us buy new versions with very little upgraded.
  23. zigidabee macrumors newbie

    May 3, 2011
    Thanks again, Germwise! :)

    Thanks again, Germwise! No need to apologize for the delay. I myself had hoped to reply to your post last week, but life and a cub scout camping trip with my son got in the way.

    Germwise, I’ve downloaded and installed the Aji pdf service as you suggested. So, now I have Endnote and Aji on my pc, and iAnnotate on my iPad. I ran Aji and a little window popped up - using the ‘add’ option I designated a folder on my pc that I created to hold my research papers.

    1. My situation is that I had already downloaded about 40 pdfs to my pc before purchasing downloading Endnote and an iPad. So, with respect to my existing pdfs, I don’t know where to start. From now on, though, I will most certainly take your advice and download pdfs via Endnote. It’s what to do with these existing pdfs that I am confused about. As you correctly surmised, Papers had changed all my named pdfs (with filenames that I created) into pdfs with ‘numbered’ filenames. These ‘numbered’ pdfs are now sitting in iAnnotate, and I used iAnnotate to give them filenames again. I am most willing to start from scratch again with these pdfs by inputing all the pdf information e.g. Title, Journal, date, authors, etc. using Endnote if this is what must be done.

    2. Thus far, at the recommendation of the iPad folks, I’ve been using iTunes to move pfs between my pc and my iPad. When I connect my iPad to my pc, iTunes kicks in and an automatic ‘syncing’ process begins.

    3. After downloading and installing Endnote and the Aji pdf service, I was hoping for some wonderful thing to happen when I connected my iPad to my pc, the iTunes ‘syncing’ process started as usual, but nothing else seemed to happen. When you stated, "In this way, any new downloaded papers on my computer, appear in my ipad and when I annotate, those PDFs automatically update the "virgin" pdfs on my computer.", I was hoping that the 'syncing' process was an automatic one, hehe. No message popped up saying that iAnnotate wanted to ‘talk’ with Endnote, or vice versa. As a test, I made a new annotation on a pdf in iAnnotate, thinking that the change would somehow be reflected in the ‘virgin’ pdf sitting in the folder I pinpointed with the Aji service. However, when I opened up the ‘virgin’ pdf, it did not reflect the change. So, I’m obviously doing something wrong, or I’ve not yet got a handle on what ‘syncing’ means or how ‘syncing’ should happen in this context. Is it something I need to do, or is it automatic? Is it because the three partners involved: Endnote, Aji and iAnnotate have not been set up properly, or perhaps I’ve missed a setup step?

    Germwise, I’m certain you’re very busy – my apologies for taking up your time with this. However, if you can help this technologically-challenged researcher out with this final piece of the puzzle, it would be greatly appreciated.
  24. maclaptop macrumors 65816


    Apr 8, 2011
    Western Hemisphere
    For the time being, I'd given up on using my iPad this way. I'm too fast and comfortable with a MBP for my research. I tried to adapt to using my iPad but it was so slow.

    Now after reading this thread its given me some new ideas to try, so I'll give it one more chance.
  25. jonsims macrumors newbie

    May 15, 2011
    What's worked for me...

    Hi everyone,

    This is a great thread! I'm a PhD student and have been struggling for over a year to turn my "toy" iPad into a useful productivity tool. I've tried many of the methods suggested in this tread, and have finally stumbled upon a workflow that works for me. It's similar to those mentioned earlier, with a couple tweaks:

    1. I've moved my entire EndNote folder to Dropbox. I have only one "master" EndNote library - so I'm not sure how this would work with multiple libraries. After this move, EndNote on my mac works EXACTLY as it did before, but now I have the comfort in knowing everything is also being backed up in the cloud... and...

    2. I've discovered a very intuitive PDF annotation program called PDF Highlighter. Boring name, great product. Here's a link: I've tried many of the others, but felt that iAnnotate's UI was lacking, and found GoodReader - while excellent - had just too many bells and whistles. PDF Highlighter has two tricks up it's sleeve. The first is SEAMLESS Dropbox integration. Go online, pull the PDFs you need, highlight and annotate, and resave to dropbox. When you pull them down on your mac, you'll see all the changes. The second trick is something I haven't seen before... hit one button on your iPad, and PDF Highlighter shows you all your highlights in one screen. Great when you want to review what you've found important.

    I've played around with Papers, and while it looks pretty, I'm too tied to the ugly EndNote because of CiteWhiteYouWrite. Thompson-Reuters is not very innovative... EndNote is five years behind the game in terms of UI and new features... but sadly what it does, it does well. I will pray that they come out with a companion iPad app, but I'm not holding my breath.

    I hope this workflow benefits some of you. I'll watch this thread to see if there are any new ideas!

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