PDF annotation app for scientific papers

Discussion in 'iPad Apps' started by LisaNewbie, Apr 7, 2011.

  1. LisaNewbie macrumors newbie

    Apr 7, 2011
    Hi all,

    I am looking for a good app for my iPad for reading and annotating scnientific papers. It should at least have the following properties:

    1. dropbox integration or another possibility to exchange files easily with my desktop (also for folders with many files so one by one transfering is not desirable)

    2. possibility to mark text by freehand (rather than selecting the text you will mark - too much of a hassle)

    3. possibility to easily set color and thickness of pen and marker before (not after) writing/marking

    I have tried UPad but it failed for number 1.
    I have also tried goodreader but it failed for number 2 and 3.

    Does anyone know the right application for me? Thank you very much!
  2. AbeFrohman macrumors 6502


    Mar 18, 2011
    Have you looked at iAnnotate?

    Does dropbox, handwriting, flags, bookmarks, etc.
  3. LisaNewbie thread starter macrumors newbie

    Apr 7, 2011
    Thank you for your reply! I have considered iAnnotate but assumed that there is no freehand marking and you always had to select some text and then choose the color in which to mark it.

    Is this correct or can you do freehand marking after all?
  4. archdelux macrumors 6502

    Oct 12, 2008
    I am looking for a similar app but require it to have a search feature to find text in the PDF...can't seem to find one either..so far I am using upad for annotations and iBooks to search but that is far from ideal..

    Maybe you could Try to use upad free /etc plus dropbox app so that you can import files into upad as needed...
  5. matt90036 macrumors regular

    Oct 9, 2010
    no it is not correct. i just used my finger to write big M, J and Y next to stuff that me and my team had to present. so free writing is there. it is one of the best PDF viewers and editors out there. it also renders large PDFs much faster and smoother than others. goodreader is only now used by me to transfer movies from iCab.
  6. matt90036 macrumors regular

    Oct 9, 2010
    thats exactly what i needed as well. im a medical student and i have loaded several PDF book into iAnnotate which were then indexed for fast searching.
  7. archdelux macrumors 6502

    Oct 12, 2008
    Ya same situation... But with iannotate don't you have o select the text and then select highlight or can u freehand highlight like in upad? I kthink that's how it works in good reader which rules that out for me..

    Any cheaper options?
  8. matt90036 macrumors regular

    Oct 9, 2010
    you select highlighter and you highlight whatever you want to. same goes for a marker/pencil. there is no need to select text before highlighting anything.
  9. katyoshi macrumors 6502

    Oct 11, 2009
    Honolulu, HI
    Hoes this compare to PDF Expert by Readdle? I'm curious myself and I'm nearly in the same situation. I have good reader btw.
  10. LisaNewbie thread starter macrumors newbie

    Apr 7, 2011
    I'm sorry, what I meant was freehand highlighting. Is this possible too?

    Also, I was wondering how I could combine UPad with a better filesystem app eg. Dropbox as suggested earlier. I am actually satisfied with the annotation possibilities in uPad but not with its filesystem...
  11. AbeFrohman macrumors 6502


    Mar 18, 2011
    Yes - you can freehand highlight in iAnnotate.

    I find that a combination of bookmarks to get to specific portions of a large document, with the note function to put my own (fairly extensive) notes about a portion, along with highlight and freehand text really gets the job done.

    For example - criminal defense case file with hundreds of pages of police reports, transcripts, etc.

    Bookmark for each officer's report to get to it quickly. Bookmark for each witness' statement.

    Notes within those reports for specific portions (notes to myself to cross-reference another witness' statement, physical evidence contradiction, thoughts, arguments and issues) and highlighting of specific portions to make them stand out.

    YMMV, but I'm sure you could find a system that works well for you. iAnnotate has some pretty good tools.
  12. katyoshi macrumors 6502

    Oct 11, 2009
    Honolulu, HI
    Is it a waste to have all three: Goodreader, iAnnotate, and PDF Expert? Or could you say they have synergistic "tech-physiological" properties? :D
  13. matt90036 macrumors regular

    Oct 9, 2010
    i havent tried PDF EXperts but i dont trust anything made by Readle. i use iAnnotate as my primary PDF organizer, reader and Goodreader only to transfer filew bwetween iCab and other apps.
  14. archdelux macrumors 6502

    Oct 12, 2008
    Why not?
  15. Readdlemate Suspended


    Jan 26, 2009
    Yeah, why not?
    We have to-notch apps and we invest heavily in technology and support.
  16. bigwinnerx macrumors member

    Mar 11, 2011
    I have UPAD, but I can sense the organization of the PDFs is going to soon get out of hand as soon as I have more than 9 files. And native dropbox support isn't there. Considering iAnnotate and I like PDF Expert devs being on here.

    Honestly feel like a chump admitting it, but, next one that drops below 9.99 will probably get me to bite. Not a super user, just want something simple that works.
  17. thunderbunny macrumors 6502a


    Jul 15, 2010
    Cheshire, UK
    For organisation of papers I go for Papers. Desktop version is not cheap though and haven't purchased yet. Can only add general notes to papers rather than highlighting specific bits of text (though I may be wrong). not a problem for me, if you read and understand the papers you are collecting.
  18. archdelux, Apr 12, 2011
    Last edited: Apr 12, 2011

    archdelux macrumors 6502

    Oct 12, 2008
    agreed.. iannotate and pdf expert seem the same to me.. maybe the Readle liason on here can help us differentiate...

    basically, I want an app that will:
    1. Handle large (often 200MB+, 500+ page textbooks) smoothly
    2. allow me to search the text of the PDFs (before, during and after my annotations)
    3. allow me to annotate via highlighting with my finger/stylus
    4. allow me to organize my PDFs in folders or tags or something else (not just random files)
    5. bonus would be dropbox integration, able to search and load Word docs/etc, ability to start new notes on blank pages, etc.. (but #5 is not required)

    So far it seems that iannotate and PDF expert are the only apps that can do the top 4 (not goodreader (no finger highlightin), or Upad (no search), etc).. is this right?
  19. mrrish macrumors regular


    Feb 14, 2008
    As a medical student, I am a huge proponent of PDF Expert--solid file and folder syncing with dropbox and a handful of other popular sync services. It has simple, well-laid out tools and I strongly believe it will satisfy all three of your requirements.

    Just to note, I also purchased iAnnotate (as well as over $50 in other "note taking" apps) and while iAnnotate has more features, I find the lack of proper dropbox syncing and messy text annotation tools the reason I go back to PDF Expert each time.
  20. Readdlemate Suspended


    Jan 26, 2009
    PDF Expert for iPad

    Hello again guys,

    I would gladly jump into this conversation.

    If you been with Readdle for a while, you know that we always listen to you and continually improve our products.

    Now, I will answer your questions about PDF Expert for iPad:


    PDF Expert is a swiss army knife for PDF documents and file management on your iPad. It combines rich set of features with simplicity of UI and navigation.
    1) It will handle big PDF easily, especially if you have the new iPad, which makes PDF Expert super fast.

    2) We did file transfer as easy as possible by giving a variety of options: 2-way Dropbox sync (the unique feature: works like charm. Let's say we're working on a new project of Facebook client for iPad. I had a flight, so I decided to work on board. All I had to do is a couple of taps to get all those files from Readdle Dropbox, you log in, chose folder you need and press 'Sync' - voila! you have all those files on your iPad. Moreover, if you add files from iPad to that folder, it will automatically upload into Dropbox), cloud storages, e-mail, direct wi-fi transfer and Readdle Storage (free 512 MB if you register yourself).

    3) You will have the ability to search inside PDF files. Additionally, you will have annotation summary, so you can quickly jump between your annotations within the same documents (very good for students, who read academic papers and writing essays).

    4) You will be able to annotate in 2 ways: using your fingers/stylus or by selecting the text. While using finger annotation (free-draw) you can chose color, size and depth of a marker. The main difference with iAnnotate here is that this works intuitively and easy, without cluttering the UI and giving tons of settings.

    5) PDF Expert also combines all qualities of a perfect file manager, so yes, you will be able to organize files in folders, rename, move, copy, etc.

    Moving to unique/core features:

    -PDF Expert lets you to Fill in PDF Forms and submit them
    -Flatten annotations, so your annotation will not be edited (useful for business)
    -Signature support (for example: I received IO from MacTech director, I had to fill it in to get advertisement in their magazine and web-site for PDF Expert for iPad. I tapped on 'signature' at the place I wanted it, and it automatically appeared there: I had previously created my signature in PDF - you have to do it once, it will be in the memory, but you can always edit it; useful tool for signing contract with customers, agreements, etc.)
    -Text typing (same case with IO, I had to put my name in the agreement, I just typed it in)
    -Recent tab makes it easy to navigate between the files you've recently opened

    Also, we have: live/static forms, auto-save annotations for crash resistance, print, e-mail annotation summary, Save as button (as copy, as flattened, stamps, sync improvements.

    There are much more ways in which you can use PDF Exper for iPad.

    So yes, PDF Expert for iPad is different from competitors. We managed to save clear and intuitive UI, while adding some core and unique features.

    I use it daily tbh. :)

    Few more words about our plans. As you know, we always improve our products, PDF Expert is not an exception. So, we are working on version 3.0, which will be the biggest update:
    -Insert images into forms
    -interface changes
    -created pdf forms from Word
    -efit pages of PDF files
    -much more, will not disclose it yet - competitors are watching :)

    I hope it helped a bit.
    If you have any questions - feel free to ask, I will try to answer all of them.


  21. caubeck macrumors 6502

    Nov 2, 2007
    PDF Expert is good, UPad is good. iAnnotate's UI annoys me, I don't like its button layout and wish it had a cleaner interface. The new eNote Taker, which I downloaded today, looks promising and is cheap.

    I like how Adobe Reader lets you choose which buttons to display in its margins, so I don't crowd my toolbar with options I'll never use. I wish iPad apps did the same. A smorgasbord of little buttons leaves me dazed and arcane symbols popping up over a text don't impress me much.
  22. lillumultipass macrumors member

    Nov 19, 2008
    Thanks Denys for these explanations! I was not aware that pdf expert allowed for Dropbox-syncing, something that I really like in Goodreader!
    However, given the differences in price tags, I still wonder why I should get pdf expert. The thing that irks me the most in Goodreader is the lack of tabbed browsing.
    I am pretty sure pdf expert does it right?
  23. Readdlemate Suspended


    Jan 26, 2009

    Well, it is personal choice what to use.. :)

    I, after trying all (iAnnotate, GoodReader and PDF Expert), am using PDF Expert because of its simple UI (clear, easy to annotate), ability fill PDF forms (I have to do surveys and submit them) and Readdle Storage/ Dropbox.

    I am not saying that GR or iAnnotate are bad. In fact, basic functions are similar, but each app adopts different approach, focusing on specific aspects.

    We do believe that any application should work flawlessly, require minimal learning time, combine powerful features which are going along with interface and good customer support. That's what we did with PDF Expert :)

    We did not do 'Tabbed browsing' for purpose. The reason is that it slows down the whole application (especially on big files) increasing the risk of crash and lags. That's why PDF Expert is faster than iAnnotate. To overcome this trade-off, we did 'Recent' tab, where you can access 5 most recent files (requires 2 clicks, 'back' from your document and one to choose the file).

    Did it help?
  24. lillumultipass macrumors member

    Nov 19, 2008
    @readdlemate: thanks, it does help!

    I understand your concern regarding tabbed browsing, above all given that it should work on multiple devices. However, I think an iPad 2 should be able to open multiple pdf files at the same time.

    Given that I don't need to fill forms, I will probably stick with goodreader until pdf expert implements tabbed browsing...

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