Filed under: Software, Education, Beta Beat
Papers: Scientific Papers PDF Manager
Papers appears to be an interesting application for those in the scientific community who need to read and manage a large number of papers as PDFs. It integrates with the online NIH database PubMed for searching and downloading. It allows you to organize articles not only by title but by author and journal. It even includes a full screen reading mode. There is nice review over at Infinite Loop by Jonathan Gitlin discussing how Papers has improved his own researching workflow.
The idea behind Papers, basically an iTunes or iPhoto for PDF journal articles, is a really good one, but I really wish it could be expanded in several areas. First of all, it clearly needs to support more online bibliographic databases and journal archives. As a humanist, for instance, I'd love a front end for JSTOR and the Philosophers Index (though perhaps I should not hold my breath since the developer calls Papers: "your personal library of science"). Secondly, and more importantly, I'd like to see Papers or a similar application offer a robust system for highlighting, comments, annotations, cross-linking etc. That's what I really need: a good tool to help me read articles (including and especially saving my notes), not just allow me to organize them.
In any case, if you need to manage professional journal articles Papers looks like a good start, though I did run into some bugs. It is presently available as a "Public Preview" and can be downloaded from mekentosj.com. It will eventually sell for €19 (~$25).
Thanks Tim!
Reader Comments (Page 1 of 1)
Fancy said 12:38PM on 3-20-2007
Sente, although more expensive, is an excellent alternative that seems to have devoted developers. It can be used as a front for JSTOR, presuming you have access to it. I use it to organize my academic pdfs and bibliographies. Great Mac style to boot.
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George said 1:02PM on 3-20-2007
Tim, what you need is a bibliographic management tool - there are quite a few out there, some even help you format your own paper with a decent bibliography. The serious bibliograhic management tools allow you to connect to and import from hundreds of databases, whether it be in the Arts & Humanities, Social Sciences, etc.
One of the most established ones would be EndNote, but I feel it is bloated to a certain extend and it makes me use one computer only. I recently started using a web-based tool "RefWorks", which works just fine for me. It allows tagging (or adding descriptors in their lingo), sorting stuff in folders, quite decent searching, it links via our library's SFX Server to full-text and it imports from all the resources I am interested in.
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Sam said 2:36PM on 3-20-2007
I'd also like to have an application that combined Papers functionality with the ability to annotate PDFs in a smart way. Unfortunately, I think Apple's PDFKit implements annotations in such that after you save a PDF with a note or circle or whatever, you can't delete it. Try it out with Preview.
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joanna said 2:58PM on 3-20-2007
I'd like to recommend Bookends. I used to use EndNote, but it would crash my computer regularly. Bookends allows you to organize and store your references. It will also allow you to launch an associated pdf in in Acrobat, where you can highlight, comment, etc. to your heart's content. I agree that an app that can do bibliography management, reference database, and article annotation in a single environment would be excellent
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Trevor said 3:28PM on 3-20-2007
I still prefer BibDesk, which is free.
http://bibdesk.sourceforge.net/
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Lars P said 3:30PM on 3-20-2007
I've been using Papers for about a month now, and I will highly recommend it for anyone in the medical science field. Endnote is a necessary evil because I need a reference manager (it would be great if Papers worked this into a future version).
A few points to add: you can do your Pubmed searches, link to the journal website and download the PDF all from within papers - think of it like the iTunes store for medical publications. You can match your existing PDFs to their Pubmed entries and add the metadata with the click of a button. You can read PDFs in fullscreen mode. And my favourite option is creating smart folders of PDFs, just like smart playlists in iTunes.
MekenTosj make some other great science-specific apps that I use all the time and highly recommend.
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Jose said 3:30PM on 3-20-2007
WOW!! That's all I can say about this software.
I'm currently using EndNote but this is so much better. Only one thing left to be the perfect software: it needs to manage references within Apple Pages or MS Word documents (otherwise i don't see much point - i would have to keep duplicate libraries; one in this program for everyday use and EndNote for writing papers)!!!
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Allan said 3:31PM on 3-20-2007
I know this is going to sound heretical, but this exact issue is what drove me back to, dare I say it, Windows!
Let me explain. First off, I'm by no means a MS fanboy. If anything, I love my Mac and all things Apple. That's why I read this site. However, I'm currently working on a dissertation in French and was tired of printing all the different articles out. I wanted a solution that could be contained all in one place as well as all of my notes. An excellent Mac program, which you probably know is DevonThinkPro. It's great at keeping everything in order. Last year, I used it to write my first chapter, wiki style. Very nice.
But then I picked up a Tablet PC for pretty cheap on Craigslist, and discovered OneNote 2003 and then OneNote 2007. To make it short, now I can print pdfs to OneNote then use the pen to highlight, take handwritten or typed notes, and move back and forth quickly between notebooks. I also use it for organizing the classes I teach and for taking notes during conferences, etc. I've also scanned books to pdf so that I can highlight them and have them with me. All my pdfs, all my notes, all my projects, all in one place.
While I still use my Mac mini at home as a repository for all my media files, I get most of my work done on the Tablet. Until Apple comes out with something akin to the Tablet and OneNote, I'll have a hard time switching back exclusively to a Mac.
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Ross said 4:48PM on 3-20-2007
Uhhh... Isn't pubmed for medicine? Not that that's a bad thing, but that certainly doesn't include general science. If one were trying to develop such a manager they would, at a bare minimum, integrate with http://arxiv.org . Of course, Bibdesk (plus a couple of applescripts) will already do that for free.
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Philipp Clemens Gérard said 8:12PM on 3-20-2007
Very interesting indeed, but also very buggy at the moment.
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brad said 9:18PM on 3-20-2007
I was looking at Yep for managing my PDF files, and while it looked promising it has a much smaller feature set than I'd like. I looked at Papers a couple of days ago and not only does it do much, it promises to do much more. The one advantage of Yep is strong scanner support. I haven't seen where Papers is looking at that, but I haven't spent a lot of time at their site yet.
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Stuart said 3:36AM on 3-21-2007
Papers certainly looks very nice and uploading a pdf seems to be pretty easy. However, I wouldn't switch from using Endnote as I need a program that can insert references into a manuscript in one of numerous styles (stipulated by the journal). Endnote is compatible with Web of Knowledge, which is another major way of searching the scientific literature. I have my pdfs linked to the reference in Endnote, which is searchable, and this works fine. I currently use Endnote 9.0 on a Powerbook G4 and experience no problems with it.
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Juan Nunez-Iglesias said 7:53PM on 3-22-2007
Ross,
Read the FAQ in the developers' website. They are from the life sciences so they started with PubMed -- they will integrate the other major databases once they hit 1.0. If they'd done arXiv first, you'd have a bunch of biologists (myself included) complaining on this site that PubMed integration is a must. It's a Beta people, so treat it as such.
Finally, to the many proponents of Endnote and/or other bibliography managers as a replacement or addition to Papers -- note that Papers aims to complement and integrate with these tools -- not replace them. As it is, Papers is compatible with Endnote, RefMan and BibTeX.
Oh, and a Tablet Mac + "iNote" would be absolutely awesome and something we are all waiting for. I imagine Apple is hard at work with one that will mimic and expand on iPhone's multi-touch interface, and thus make PC tablets look dated and ill-conceived in comparison. =)
Juan.
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Ben said 1:06AM on 4-03-2007
Great App!
Does anyone know of anything similar that handles legal databases (ie LexisNexis or Westlaw)?
Any thoughts would be MUCH appreciated.
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