I am going to be purchasing software to manage a library of monographs in PDF format. The programs I am aware of that exist are:
Since I am starting from scratch, could anyone give me their input regarding which one would work the best? I do also need to reference my monographs in citations, which presently makes Endnote look the best, since my main word processor is Pages and it supports Endnote.
Is there any major advantage or interoperability planned or working right now, with DevonThink and any of the previous four?
I like DevonThink very much, but I do need a specific program to manage monographs which will automatically get citations from Pubmed, Google scholar, etc and allow me to cite them using either Pages or Word (preferably Pages).
I would also like to index the entire library of monographs from one of the above, into DevonThink. Again is there any particular one out of those 4, which works the best for this?
I use Papers as a front-end to search for, well, papers! And bookends (which I got for free) to easily create bibtex files. I have also played a bit with the demo of sente. But I hasten to add that I do not use citation managers to manage citations; I put them in by hand mostly (I use LaTeX).
Having said that, Papers, for instance, can be set up to save all the pdfs into one folder; one can then set up a folder action that automatically indexes (or imports, but that uses up more disk space while making things more robust with respect to filename changes) pdfs added to the relevant folder.
That is, it is easy enough to set up DT so that it automatically indexes/imports a given folder; thus, if one uses a citation management program that stores all the pdfs in a folder, one can set up things so that DT is always up to date.
Thus, any program that saves all pdfs into a single folder will work (Papers can be set up to do this). I am not sure how easy it would be to arrange things so that DT automatically synchronizes all folder under a given folder (if you were to use a citation manager that uses subfolders with dates or author names, for instance). It could perhaps be done with scripts but I haven’t tried.
I have tried all of those softwares (and bought Papers in fact). At the end I ended up using just Zotero + Bibdesk. ( I also use Latex) One other separate program for keeping and viewing PDFs just made my world more complicated.
The biggest decision I made was to separate the PDF and the bibtex worlds. I am not accessing PDF files through my bibtex file, I just use it to enter references to my Latex file. For the PDFs I use DT.
Anyway, this is what I do now:
Pull the reference entry from the web with Zotero to a bibtex file stored in DT. And if I am going to download the file, download it to the associated folder in DT. (Of course first into Inbox, then move it to its folder at the end of the day.)
While writing the paper, open the bibtex file with Bibdesk and drag the entry from Bibdesk to my latex file. If I have to add something from google scholar I can also do it right from Bibdesk.
This works for me for now. But of course the greatest improvement would be a more direct interaction between Zotere and DT !
This is a tough nut to crack. Each application mentioned has its own advantages and disadvantages. Nothing can substitute for each individual user’s trials and explorations of the available alternatives.
A few general assessments can be made, however.
Among the large stand-alone applications (Bookends, Endnote, Sente), Endnote is by far the worst. Endnote is simply unable to handle several citation and bibliographic styles correctly, especially those involving footnotes. If you are in the humanities, especially, stay away from that dinosaur. I personally fail to understand the commercial success of this application.
Bookends has been around for approximately 15 years. It’s the software I use every day. There’s very little that you cannot do with it, but you’ll have to tolerate a user interface with more rough edges than you can imagine. I mean details like keyboard shortcuts—which are often different from the standard ones used in Mac apps—and a generalized and intriguing lack of compliance with application behavior guidelines (e.g. triple clicking on text selects that line of text rather than the entire paragraph). There is an overriding advantage, however: Its absolutely STELLAR support. I don’t think there is any other software, in ANY category, which is nearly as impressive as Bookends in the support department. Do not underestimate the significance of this! Having a paper due in 2 days and facing a major issue with your bibliography can be tormenting. Not with Bookends: you just write to Jon (owner) and rest assured that an answer will be delivered in a matter of hours if not minutes. This is just incredible. Again, I urge you to consider real-world scenarios and realize the importance of immediate technical support. Bibliographic management is rarely uncomplicated.
Bookends also boasts a number of features that are unique among bibliographic managers, certainly more features than I can enumerate here, including many that you will likely never use. If you don’t mind the clumsy and eccentric user interface, go for it.
I have been extremely tempted by Sente. It looks beautiful—in fact, it’s the only bibliographic application around that looks like modern Mac software, and the only kid on the block with a visual styles editor, which I consider a major innovation. If I were starting from scratch, as you are, I would have seriously considered Sente because I am very sensitive to user interface glitches, and Bookends fails miserably in that respect. On the other hand, Sente has several significant drawbacks: It is quite buggy, allegedly crashing all too often. Support is HORRENDOUS, with tickets remained unresolved (or even unanswered weeks or months after submission by the user!). And for serious work with large databases, you may find some essential functions missing.
To summarize: Endnote is out—no compelling reason to buy. Bookends is the best choice if your data set is large and you expect rock-solid stability coupled with unprecedented support. Sente is a very interesting solution but also a risky commitment at the moment: Very beautiful and intuitive, but you may have to deal with the occasional crash, the lack of more esoteric features, and an infuriating customer support team (if there is one at all).
I have never used Bibdesk so cannot comment on that.
Zotero is a very promising solution but currently inadequate for all but the simplest needs. If you need to tweak your bibliographic styles forget about it. Support for major word processors such as Mellel and Nissus is also missing. And there is no way to handle reviewed items properly—again, a serious problem if you’re in the humanities. Unless you are just experimenting with new technology, you should bite the bullet and buy a standalone application.
Added later: I would now recommend Sente 6 over Endnote X3. I had a 4-person collaboration and one had an emergency trip out of the country. I had his paper, but many of his references were incomplete and the deadline was looming. I had gotten the Sente 6 upgrade, but hadn’t used it yet. I did need a bit of help, but that went quickly and smoothly. I imported my Endnote file, used Sente’s reference search capability–which was spectacular–and in a couple of hours was able to integrate all the references and send the manuscript. Although I expected that I’d re-import my references to Endnote after my search, it was such a pleasure to use Sente 6 that I’ve stayed with it.
For my use, I’ve found Bookends and DTPro are wonderful.
E.G., I keep a sub-folder in my attachments folder in Bookends with PDFs related specifically to a topic/article I am writing. I have linked DTPro to this folder. While in DT I can annotate extensively and the annotations appear within Bookends to remind me of what sources I’ve gone over. Bookends also plays very well now with Nisus Writer Pro which I also use.
I would also second the support of Bookends: it is absolutely fabulous: fast, polite and quick. Jon, the developer, has been very aggressive in incorporating user suggestions.
I don’t find the interface particularly idiosyncratic (see above), and certainly the latest version of BE is rock solid and, I think, attractive.
I have been using Sente for over a year, starting with version 5 and now version 6. I was an endnote user for a long time switching to Zotero for a short while. However, I discovered Papers and Sente. At that time I found Sente superior and bought it. Superb interface, easy to use and you can cite directly in a number of word processors. Sente is also one of the best tool to archive and retrieve pdf articles (I have over 2000 of them). It has many more options (automatic search, …)
I have not been using “blundles” for my library but rather folder and files. This is to make sure that Sente and DTPO play nice together; I index (and automatically update via a script) my Sente folder in DTPO.
I’ve been playing with Mendeley (mendeley.com/) together with DTP for a month or so now, and they work reasonably well together. The only thing that I’d really love is to find a way for the two programs to share tags.
The various programs are so different that I would suggest that anyone who has the time should download and try all of them. I think often people find that the one that has the best list of features is not necessarily the one that feels right, perhaps because of one or two things that are so well designed (or match your way of thinking) that you use them frequently.
A few comments on each program:
Papers is, “on paper”, clearly the worst choice (it doesn’t even do reference management as such!; they get around this limitation with a Send to Bookends command). Yet it has full-screen PDF viewing, and is the only program to have an iPhone/iPad/iPod touch companion app. It has a Safari extension that puts a Send to Papers button in the toolbar: this opens the page you were looking at in Safari in Papers (say the abstract page for a paper), where you can click the download PDF or similar button, which will be associated with the correct article. It’s also very Mac-like, and is the only app that allows you to drag a PDF onto its Dock icon to launch the app and import the PDF.
Mendeley has apps for Windows and Mac, and a website, and your collections in all places are kept in sync. It’s the only one where not having your own computer available isn’t really a problem. Mendeley for a time had an amazing feature whereby it would parse the reference list at the end of papers and list them in the program ready for you to import them. That has been taken out temporarily because it had a lot of errors, but I think it symbolizes the innovative thinking they’re bringing to this software. If you work with other people, Mendeley’s shared collections are also hard to beat: anything that any member puts in there is automatically shared with the other members.
Bookends has great support and is the most mature of the various contenders. Despite its old-fashioned look, it is the only one of these programs to sport tag clouds, which to me seems an incredibly obvious and useful feature, but nobody else has seen fit to do it. It’s also the only one to integrate with CiteULike.org.
Sente has great notetaking/annotation features. It also has an interesting sharing/synchronization system. And an iPad version is reportedly coming soon.
I feel that annotating PDFs on my iPad is a very good use of time and creates a nice divide between “working at the computer” and “reading on my iPad”. Papers is my only choice now. It’s nicely designed and annotating is fairly pleasant, but they haven’t yet worked out how to sync the annotations back to the Mac. Things will be interesting when Sente for the iPad comes out. I think I’ll probably end up going with whichever one of those is first to create an iPad app that is stable and allows syncing of annotations back to the Mac.
Another quick update: The Sente people have submitted a Sente Viewer app to the app store, to tide us over until the full version. I think we’re soon going to have two viable alternatives for working between the Mac and the iPad: thirdstreetsoftware.com/blog … -ipad.html
Oh, and looking at the comments on the post linked above, it sounds like Mendeley has an iPad viewer app, too, which I had completely missed.
Using Bookends, downloaded Sente, the note taking annotation compared to BE NoteStream seems rather basic , has any body used the two and can give us a more detailed comparison, the only thing that prompted me to look at Sente is the the upcoming ipad version, and now DT link.