Why I use BibDesk instead of Papers

by Kelle on October 29, 2009

Bibdesk
PapersFolks have been clamoring for a Papers vs. BibDesk post and here it is, finally. Since I don’t actually use Papers, this post is more of a listing of my reasons for sticking with BibDesk for the time being. This topic has been discussed elsewhere and is sure to be visited many times in the future on AstroBetter, so consider this post just one part of a much bigger discussion.

There are different things to look for in an article management tool. I want my app to be as one-stop shopping as possible: I want to be able to search, import, organize, assign BibTeX cite keys, and annotate all in one place. BibDesk does most of those things while, as far as I can tell, Papers really only excels at searching and importing. Papers gurus, I’m counting on you to speak up in the comments if I’ve missed something. Below, I’ve listed the main functionalities, in rough order of importance to me, and which application I think handles them best.

Keywords/Tags: Bibdesk
Keywords play a starring role in BibDesk, occupying the left column in the main page while in Papers they are hidden in Notes. With BibDesk I can highlight multiple articles and quickly specify if I only want articles with ALL of those keywords, or papers with ANY of the selected keywords. This ability to easily tag articles with multiple keywords and then search based on them is a huge advantage of BibDesk over Papers but I think Papers will catch up soon.
PDF Annotations: Bibdesk + Skim
Annotations added in the PDF reader app Skim show up as Notes in BibDesk so you don’t even have to open the PDF to see the text you’ve highlighted or underlined. (Skim vs. Acrobat vs. Preview is a can of worms that I choose to leave for another day.) Improved annotation functionality and integration with Skim is likely for future versions of Papers.
Search and Import: Papers
Papers auto-magically imports articles and metadata and downloads the PDF while importing an article into BibDesk is (usually) a multistep process. The way I do it is browse to the article’s ADS entry, scroll down, clink on “Bibtex entry for this abstract”, highlight the bibtex, switch to BibDesk, use alt-command-L to add a new publication from the clipboard. BibDesk does have a Papers-like single-click import for articles on arxiv.org, but not for ADS. Looks like this ADS to BibDesk app is on the right track, but it only works with Safari, not Firefox. Getting this functionality built into BibDesk would rock.
Cite Keys: BibDesk
BibTex + AstroNat is what you should be using to include references in LaTeX articles prepared with AASTeX. Again, a full discussion of BibTeX is left for another day, but suffice it to say, being able to assign memorable cite keys to articles is important. To be honest, I’m not quite sure how Papers assigns cite keys to new articles. BibDesk autogenerates cite keys based on a user-defined format. I’m partial to first author + two digit year (Custom format string:%a1%y). And then I just add a sequential number to the cite key for the autonaming and autofiling of the associated PDFs.
Slick UI: Papers
You gotta admit, Papers sure is pretty while BibDesk leaves something to be desired. The most recent update to BibDesk (1.3.22) helped a little, but it’s still not as clean as Papers even though they both use the same 3-column layout.
Cost: Bibdesk
Bibdesk is free and open source. Papers costs $42 for non-students, $26 for students.

Reading Papers: Papers
Papers is great for using as a browser to read PDFs. Papers even has an iPhone app ($10) which enables you to sync a Smart Collection so that the PDFs are at your fingertips when you have some dead time for reading. BibDesk is great for browsing notes or annotations, but not for reading the original papers.
(Updated Nov 2, 2009: Thanks to Marshall for pointing out this functionality that I had overlooked.)

Also consider Mendeley, which is both a desktop and online article organizer.

Alright, there’s by BibDesk biased view, let’s hear from the Paper’s lovers in the comments.

BibDesk, free
Papers, $42 or $26 for students

{ 22 comments… read them below or add one }

1 Brian S October 29, 2009 at 6:13 pm

thanks Kelle. This is very useful. It’s time I started using BibDesk

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2 Victor October 29, 2009 at 6:19 pm

I’m papers user, so here are my comments:
1)I like bibdesk very much: It’s free, fast and does more or less the same as papers.
2)While 1st is true, bibdesk is not nearly as good as papers for managing papers. It’s supposed to manage references and that’s what it does. Basically the main problem is that for every action (adding/reading/annotating etc) one needs several steps (or apple-script). As it often happens, bibdesk is a tool and paper is a “solution”
3)Sadly enough, bibtex export in papers is crap: it exports lots of non required fields+is not nice to complicated surnames (i.e. no respect to {} in bibtex). Most of my references come from ADS, so when I export bibtex from papers I run a small python script to fetch bibtex records from ADS. Actually It’s attached to a folder action and my latex template just include path to a single file containing complete library, so that’s not a major issue. Still, while I can forgive bibdesk for needing additional scripts to work smoothly, I can’t forgive Papers for this. I would not buy it if I knew this in advance. On the other hand, I tried to switch to bibdesk and found that I like papers better (after adding the script), so that’s just a money question.

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3 Oskar June 24, 2011 at 3:21 am

Victor, re 3, you can customise the way BibDesk exports stuff. Look at the templates feature, you can remove all the {}. I use BibDesk to automatically generate my HTML, PDF, even DOCX CV’s. I don’t use it for papers only, but for other type of “documents”. Some kind of academic database.

4 Josh Peek January 24, 2013 at 9:29 am

Hi Victor,

I was just having the same problem with BibTex export — are you willing to share your script? Does it still work?

5 WesTF October 29, 2009 at 6:20 pm

Just a few notes about Papers:

Papers can handle very well cite-keys. You can customize them yourselves, or have Papers do it for you.

Papers can import an existing bibtex file. I haven’t tried too hard with this one, but I believe it will also download all the pdfs from said bibtex file. That could be good or bad.

Also to note that the reason I don’t use papers, is because I do everything in quicksilver. I have some scripts I wrote to interface between quicksilver and ads-search without my browser. I also open my pdfs this way. Now that I see that bibdesk is open source, it provides the framework necessary to put together my dream – metadata, pdfs, ads search, astro-ph, and user notes, all within quicksilver, all while managing my bibtex behind the scenes. Looks like I will jump on-board contributing to bibdesk!

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6 Esme August 27, 2015 at 9:29 pm

This isn’t true any more – Papers handles cite-keys appallingly. Almost every paper I have has the cite key starting with either my name (or my computer log in to be precise) or Anonymous -> I have to manually update them and cannot check for doubleups.

They do ensure you don’t get double ups if you don’t do things manually – but you won’t have cite keys that make sense and are easy to recall when typing your work.

7 Thomas Robitaille October 29, 2009 at 6:21 pm

I actually purchased a License for Papers when I was writing my thesis, and transferred my bibliography over from Bibdesk to Papers. A few months ago, I switched back to Bibdesk.

What I like about Bibdesk is that it is very lightweight. Papers is too slow when dealing with thousands of references. I find it much easier to search for references using ADS via the web browser inside bibdesk than using the search feature in Papers. Another issue is that (last time I checked), Papers still did not allow custom citekeys. I like to use Author:Year:Page, and there is no way to specify custom keys in Papers.

Tom

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8 Gus Muench October 29, 2009 at 6:36 pm

re Bibdesk: since it auto recognizes bibtex entries on a webpage, you can use the Bibdesk internal browser to do a search on ADS. Once at the abstract, clicking on the “Bibtex entry for this abstract” on the ADS page takes you to the text page and Bibdesk will offer to import it for you.

re tags: my experience using the keywords on the left in bibdesk is not so pleasant. I tried to map the Journal keywords for a bunch of articles but this produces a unpleasantly long list of singletons.

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9 Oskar June 24, 2011 at 3:31 am

try this: say you have two keywords one named “hip fractures” (with 2 items) and the other one “hip fracture” (with 3 items). Click on “hip fractures” and modify it into “hip fracture”. You’ll get a single keyword with 5 items.

10 Eli October 29, 2009 at 7:09 pm

I’m similar to Tom about Papers and Bibdesk. I purchased Papers about a year ago and I still use it, but only for perusing my library of PDF files. When it comes to dealing with references I actually use Bibdesk to clean up the export reference file from Papers. I know, it’s haphazard, but I like what both applications have to offer.

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11 Jonathan Sick October 29, 2009 at 9:48 pm

Hi, I wrote the scripts for the ADS to BibDesk tool that you mentioned. With that script, I manage all my papers and PDFs in BibDesk and read them with Skim. Its an amazing system; I never have to print a paper, and spotlight is remarkable at finding the paper I’m looking for. I do agree that the power of BibDesk is ultimately its open-ness and scriptability.

One issue that I have is replacing astro-ph articles with the published version, once the published version becomes available. An automated tool could do this; e.g. a python script that tracks ADS’s journal RSS feeds, somehow correlates any astro-ph entries in your bibdesk database to those published, then replaces the astro-ph bibitem with the new version. I’ve thought about writing such a thing, but of course, haven’t yet had the time. If someone wants to take that on, that would be awesome.

Its probably more pressing for me to update ADS to Bibdesk’s web page parse to handle some articles that it currently fails on…

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12 Marshall October 30, 2009 at 12:34 am

I’m struck by how different what we all want out of these programs is. For me, I love Papers, but I use it almost entirely as a multi-tab browser for my library of PDFs, which it’s great at. BibTeX may be better at sorting and searching references, but I spend far more time reading articles than I do making citations. (I hardly print anything ever anymore.) I love the fact that Papers syncs with my iPhone. I sync a Smart Collection containing all papers added in the last N months flagged ‘To Read’, and I’m good to go for bus and waiting-in-line paper reading purposes.

I don’t think I’ve ever had any problems with the exported BibTeX files – I can’t imagine hand-editing to clean one up. (and isn’t cleaning up reference entries what journal copy editing staff are best at?) Rather than tagging keywords, I have various collections on topics or targets, and it’s a simple matter of drag-and-drop to add a paper to a collection (or more than one, equally well).

Tom – thousands of references? Wow. I think I’ve got around 1200 in my Papers library and don’t notice any speed issues at all.

Wes, I’d be interested to learn more about your quicksilver ADS scripts. Is this something you have written up anywhere?

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13 Carolin Villforth November 4, 2009 at 9:21 am

As my laptop is running linux (kubuntu) I can’t use BibDesk or Papers. I am using zotero which is a add-on to firefox ( http://www.zotero.org/ ). I am pretty happy with zotero.

zotero positive points:
-it’s free and it works on every operating system (as long as it runs firefox)
-articles can be imported directly from ADS, arxiv or pretty much any other page, just by clicking a little symbol that appears, you can also import many articles at a once (i.e. all results of a ADS search)
-you can create your own collections, exporting collections to bibtex is extremely easy (that means, you don’t have to export your whole library to bibtex if you write an article)
-you can add your own keywords and search by keywords
-you can attach pretty much anything to your articles
-you can “relate” articles to each other

zotero downsides:
-zotero does not have a native pdf reader, pdfs are added to the article as attachments. However, you can open the pdfs with only one click using your favourite pdf reader.
-in earlier days, updating firefox used to be very exciting as there was a chance that zotero was not compatible with the newest version. But I didn’t have any problems with that lately.

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14 Conor Mancone December 17, 2009 at 12:00 pm

One of my collaborators introduced me to papers. However I’m the sort that likes to reinvent the wheel, so rather than using it I spent a week or two making my own online reference manager:

http://www.mancone.net/refs/

The biggest advantage is that it is online, so you can access it anywhere and don’t have to install anything. It doesn’t have quite as many fancy features though (I did put this together myself after all). It has a generic bibtex importer and will fetch abstracts automatically from ads. You can browse and search the references like you normally would, and it also has a category view. You can create a category tree and put any reference in as many categories as you like, and so it acts much like a bookmarks menu. Not much in the way of documentation right now…

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15 Nico January 20, 2010 at 5:58 pm

For me, Papers and BibDesk are actually complementary. I use Papers for managing my pdf, references, etc. I just find Papers fantastic for searching within the pdfs, ior using the smart folders and collections.
Then, when it comes to write a paper, I export a .bib from Papers and fine-tune it with BibDesk. Very happy with the result so far.
A major step forward would be for Papers to recognise changes made in the .bib and have a two way coupling rather than a one way export. But apart from that, I really think that both are equally useful in their own way.

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16 Jo July 23, 2010 at 6:35 pm

One of the biggest diferences noone has mentioned is support for supplementary material. Many articles may involve more than just pdfs.
Bibdesk supports any type of file (images, docs, bookmarks) while Papers only supports pdfs. More importantly, bibdesk allows you to link all those files to the same record, which Papers still does not allow (at least easily).

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17 Andrew December 29, 2010 at 3:42 am

I have both, and use both. I love Papers for reading pdfs as many have said.

Maybe I’m doing something wrong, but whenever I export a .bib file for a latex paper, and compile using aastex and astron (or ApJ) style it fails miserably. About 60-70% of the citations are not correct for a variety of reasons. Several of my colleagues have the same issue. I’d love to say goodbye to bibdesk and do everything using just 1 program, but as long as bibdesk does the bibliography correctly, and papers.app doesn’t, I’m suck.

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18 Mike February 22, 2011 at 4:58 pm

I use the JabRef, which is java based. From the description above, it sounds very similar to BibDesk.The advantage here is that it is cross-platform, and so can run on Linux, Mac or Windows. Its native database format is bibtex.

So my solution is bibtex db plus the jabref .jar file in my Dropbox and I can carry on editing my paper whatever machine I am on.

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19 Andrea November 2, 2011 at 7:26 am

My two cents: I was a Papers fan (I even bought the mobile app for iOS). Moved to Lion OS on my Mac. I would need to re-pay to get Papers 2.0 and the old version simply got impossible to handle with freezes/instabilities. Moved to BibDesk my library (export from Papers, import from BibDesk), seems to do perfectly good what I need (in particular organizing / storing PDFs).
I consider the idea to re-pay for a (minor) update of Papers quite ridiculous. I will stay with BibDesk.

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20 A November 9, 2011 at 2:53 am

For those who use Bibdesk and Jonathan Sick’s ADS-to-Bibdesk entry, it’s worth noting that he’s now created a tool that automatically replaces Arxiv entries with the corresponding journal entries. Just run the script every week or two, and it should keep the bib library up to date. Very easy to use, and one of the last pieces missing for Bibdesk to be a perfect tool for my needs.

http://www.jonathansick.ca/adsbibdesk/index.html

The very last piece is a way to make my bibliographies list the arxiv identifier for arxiv-only entries, and only for the arxiv-only entries. I can make it show the arxiv identifier for every paper, but that’s almost as annoying as having any arxiv-only paper only be listed as “Arxiv e-prints”.

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21 Nico January 24, 2013 at 3:16 pm

This thread still seems active so a couple of updated comments may be useful. I have been a long time user of both BibTeX and Papers so my comments below are hopefully not too biased!
– Papers2 (new version of Papers) has drastically improved BibTeX support. With the previous version, I systematically had to clean my exported .bib with BibTeX. Now, it’s not necessary anymore, making the whole one-way transition from Papers2 to LaTeX essentially flawless. Still hoping for a two-way editing of .bib but that’s minor IMHO.
– Annotations are now fully supported in Papers2. Additionally, any highlighted piece of text in the pdf now automatically appears in the “Notes” for your reference. Used correctly, I found it to be a fantastic tool to create a quick summary of the main points in a paper. I use this extensively and it saves me a heck of a time. So, annotations is another area in which Papers has drastically improved.
– for MS Windows users (poor things….), note that Papers is now available for Windows too.

Summary: Papers2 has much improved after this BibTeX vs Papers review was posted. Most of the points mentioned above (and very relevant at the time), are not all relevant anymore. Since updating to Papers2, and as much as I love BibTeX, I haven’t used BibTeX at all. So if you are happy with Papers2’s price tag, I would highly recommend it, or at least check it out (trial available for download on the mekentosj website).

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22 Nico January 24, 2013 at 3:19 pm

ERRATUM: all “BibTeX” in my comment above should read “BibDesk”!That’s what caffein depletion does to my fingers (and brain…).

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