Comments on: Why I use BibDesk instead of Papers

By: Jo

Jo — Fri, 23 Jul 2010 22:35:34 +0000

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).

By: Nico

Nico — Wed, 20 Jan 2010 22:58:42 +0000

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.

By: Conor Mancone

Conor Mancone — Thu, 17 Dec 2009 17:00:44 +0000

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…

By: Carolin Villforth

Carolin Villforth — Wed, 04 Nov 2009 14:21:24 +0000

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.

By: Marshall

Marshall — Fri, 30 Oct 2009 04:34:27 +0000

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?

By: Jonathan Sick

Jonathan Sick — Fri, 30 Oct 2009 01:48:06 +0000

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…

By: Eli

Eli — Thu, 29 Oct 2009 23:09:19 +0000

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.

By: Gus Muench

Gus Muench — Thu, 29 Oct 2009 22:36:32 +0000

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.

By: Thomas Robitaille

Thomas Robitaille — Thu, 29 Oct 2009 22:21:23 +0000

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

By: WesTF

WesTF — Thu, 29 Oct 2009 22:20:10 +0000

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!