That’s fine … as long as you like or are willing to be committed to using Firefox! Me, I’m an OmniWeb person and couldn’t stand Firefox …
But then Bookends does what I want too.
Working offline is crucial. Now that I’m past the literature review stage, things are working out. I do t have to do as much article searching as before.
Like grgcombs, I’m a Papers + EndNote user.
Papers is great for finding and reading references, and for automating the generation of citation material (it can automatically look up and import citations direct from PubMed and other databases). However, it’s terrible at getting these citations into anything written. It just can’t do it.
EndNote is just awful, but it is great at getting references into written material (at least in Word or, apparently, Pages 09). It is also, if necessary, cross-platform (useful in university).
My workflow:
- research in Papers, collecting relevant articles into their own collection.
- draft, then export into final editor of choice (Word for simplicity within the university)
- export Papers’ references to Endnote
- import EndNote refs into Word
- check references, correct if needed (EndNote X APA template was wrong and needed tweaking. Haven’t checked X2 yet)
- submit
OK, there’s few more intermediate steps along the way, but that’s the gist of it.
I’m surprised more people here aren’t use Zotero. It is brilliant software in my opinion. And one doesn’t need to be online to use it. And it costs nothing. And it runs on Windows and Linux as well as Mac (which perhaps matters more to me than it will to most people on here).
Well worth a look, anyway.
All the best,
Ian
Using Zotero and very fond of it – and since FF 3.6 is nippier than previous versions on the Mac this is even more pleasant. I’m drafting in Scrivener and using Zotero’s RTF-Scan function. The workflow: (a) Writing in Scrivener; citations, if I know them off-hand, are typed in in squirley brackets {James, 1890} or else fished out of Zotero via the quick-copy feature and a defined style. After my text stands I’m (b) exporting the draft as an rtf-file and © run Zotero’s rtf-scan feature on the text. There is generally a bit of ‘resolving’ to do (d, e - y) 
The result – including the bibliography generated by Zotero – goes either into NeoOffice, where I then have a text with citations and complete bibliography all from my Zotero library (though the interop via Zotero’s NeoOffice plugin doesn’t work with RTF-scan inserted items); or to Mellel (no plugin) where the citations and bibliography are in text (likewise not live) for finer typography. The RTF–Scan feature in Zotero could (and hopefully will) be more refined but overall the process has been quite workable – sticking to the conventions while typing the citations in Scrivener is crucial otherwise they will not be recognized in the scan. Zotero, besides doing bibliography, has also become an indispensable research-tool for anything web related; it does a lot more stuff which I don’t use.
Best, kithairon
Have a look on Citavi. For the time being it is a Windows program yet. But they are working on a Mac version.
However it works fine inside Parallels or Fusion.
A really great program for not so much money.
I write in Scrivener then export to Nisus where I edit, format, and insert all my footnotes using Sente. I usually then have to export to Word as many editors work only in that 
One of the reasons I hate Word is that there are so many clumsy icons and so much stuff there that I don’t need, want nor understand that I never feel comfortable and in control of my writing environment. I feel the same thing with Endnote. Bookends I tried and liked, but Sente, for me, was very simple, clean and mac like, also, it’s pretty So I use Sente, but I don’t identify footnotes in Scriv, just write write write and sort out all the rest when I export (sometimes with the help of a research assistant).
I use Sente. I’ve tried BookEnds, but somehow I just don’t feel comfortable with it. EndNote is just too PC for me. Sente, on the other hand, works great for me. I especially love the way I can create a quotation database in it.
I simply drag and drop the references, add pages numbers, when I have to, and after I export the final draft I use the scan document function. It really works nice for me.
To find web pages and keep track of PDFs I use DevonThink (not a bibliographic software at all, but great to simply keep it all). I use Zotero in rare occasions, mainly because I need something in my PC at work. I find it buggy, and even when it has a note function, it’s not as nice as Sente’s.
This is a common observation, but I don’t agree with it at all. Because my university has a campus license, EndNote costs me $13 for a yearly subscription, and that’s all I ever pay. The latest version is X3, and there’s nothing PC about the interface or its operations. Online searches of distant libraries are easy, as are creating output styles and storing annotations, abstracts,URLs, and links to files or e-mails stored on my computer. If you love Sente or Zotero, great; but please don’t bash a program you use little or not recently.
Seems to me this issue is very much “horses for courses”, coming down to what you feel comfortable with.
I haven’t tried EndNote: out of my price range, I felt, though I can no longer be sure of that; and at the time it seemed to be very much tied to word and be Windows-like from all the comments I read, and I have been a Microsoft-free zone (apart from the necessary evil of an MSN account, though I use Adium) since OS-X came out.
I have never got on with Firefox: purely a matter of personal preference; I have been an OmniWeb user since OS-X came out, and though I have always had Safari to hand, I prefer Opera as my second string browser; so Zotero was not an issue.
So it came down to Sente vs Bookends for me; and it came down once again to simple personal preference. I found on trial, brief I admit, that I didn’t get it with Sente but I did with Bookends. So I invested in Bookends and have never regretted it.
I have also to admit that I’m anything but a heavyweight user, but as time has passed and all of them have continued to develop, from what I read, I can’t detect that much differences in ability between them. I think it’s only if you used all four “for real” on an extended basis that any differences would really show up, and who’s going to do that. I’m not in a position here in China to test out things like searching distant libraries, and am not doing anything that requires that, so I can’t comment on such matters.
And along with Druid, if I had been in an environment where I could have got EndNote for $13/year and had been able to use it, I would have taught myself to be happy with it, I’m sure.
So I stick to one, Bookends. It suits me; the library file is in a folder which is synchronised between my two computers through SpiderOak (originally the now inaccessible DropBox), and it can do far, far more than I need it to do.
Mark
I’d like to add ask a, probably dumb, question.
I’m using Scrivener to write assignments for my OU degree and the thing that gets me in a tangle is getting the citations and bibliography in the required formats. So I’m keen to acquire some software to help me. I’ve had a look at Bibdesk and Bookends. Bookends appears a bit more elegant but they both seem to insert citations and build bibliographies. So the question that I haven’t been able to figure out for myself is; am I getting anything extra with Bookends to make it worth my while paying $100? It’s got a nicer GUI but does it doing anything extra I’ve so far failed to spot and might benefit from using?
Any opinions on this much appreciated, thanks.
I can’t do a straight comparison because I don’t use Bibdesk. (I tried it a few years ago and it didn’t do very much, but I expect it has improved since then.)
Bookends can do some things that no other reference manager seems to do. One example: you can link references so that if more than a specified number of papers from one edited book are referred to, then the book is added to the bibliography and the listing for each paper is truncated, automatically. There are other examples. Bookends is very frequently updated, with new features continually added.
Still, unless you make heavy use of some particular advanced feature, I think the important things are the general usability of the application and the level of support available. Bookends is unmatched in both areas. There’s a free trial available, so you try it out and see if it works for you.
(Usual disclaimer: I have no connection with Sonny Software except as a long-time user of Bookends.)
BookPedia is worth a try, and it’s only $18.
Plus:
Finds books quickly from online databases
Many fields for organizing and sorting data
Edits multiple fields rapidly (get all publisher names in same format)
Exports in EndNote and BibTex, or create your own templates
Minus:
Not great for listing articles
I start with BookPedia, export to EndNote, and use it for adding articles.
I’m a Zotero user. It doesn’t look as pretty as some of the other packages, but it’s certainly powerful. I wish it integrated with Scrivener (though I understand why it doesn’t at present), but kithairon’s tips may prove very helpful. Thanks!
If you don’t use Firefox, I would still recommend looking at Zotero. It is a fully featured piece of software in itself, even though it runs from inside Firefox. All files (including webpages) are stored locally so you can look at them offline; this also helps if a webpage changes or vanishes after you have referenced it. You can find a book in websearch (on Google Books or in the BL archive) and add it to your sources with a single click. It also does the normal filling in of catalogue details from an ISBN / ISSN number etc. The bottom line is: while you are using Zotero, the software feels like a bibliography manager with built-in web browser, rather than the other way around.
From my perspective, Zotero is actually a reason to install Firefox, even if you don’t want to use it to browse the web.
And… it’s free!
It looks like there are many bibliography and reference applications that will work and Scrivener seems flexible in which of them to use (you can just select any one in Preferences and CMD-Y to open). From the long list of Sente, Mendeley, BibDesk, Endnote, Bookends and so on, Scrivener users are not short of options. I tested Sente (trial) and Mendeley (free). Both of them work well by just dragging and dropping the reference from the bibliography manager to Scrivener draft. That is great. For the citation, I guess the user just has to write it manually. I can’t see another way to do it, but at least all the references are there in the same format.
I can’t quite figure out why Scrivener and DevonThink don’t have built-in bibliography and referencing tools. It seems like it would be much easier to reference and then it will add that document to the bibliography. Anyway, the point is they don’t do that as far as I can see.
Although the Mendeley-Scrivener seems to be good enough, what I don’t like about it is that there are two copies of the document on my computer: one in Mendeley, which is just referencing the document that sits in a Finder Folder, and one inside the Scrivener database. This means every time I add a file, I have to add to both Mendeley and Scrivener… or worse, also to DevonThink, which I can only see having application to store All documents and acting as a central storage warehouse, which it seems to me is only fractionally superior to using the Mac FInder and Spotlight.
Am I missing something here, or is there a better way of doing this? I would love for both Scrivener and the bibliography manager to draw from the same file.
Because it is often better to integrate with specialists than for every single program that has anything to do with writing or storing research to all reinvent their own wheels. This way you get many dozens of programmers creating unique alternatives that work with a wide variety of workflows, from RTF files to LaTeX files, with broad support for various citation styles, to the user’s taste when it comes to how applications should work—instead of one single, one size fits all, watered down version of the same. This is especially true when the specialist applications are written by single developers or very small teams.
I’ll leave the rest of the post for others with more experience with this software, but do highly recommend developing and acclimating to workflows that encourage the integration of specialist tools. I’ve found it to be a very rewarding way to increase what I can do with a computer; it’s very reliable because individual parts of the workflow can drop out and be replaced if necessary. One lost software doesn’t destroy the entire workflow; it promotes standards-based data that is open and easy to use as time goes by instead of locked into proprietary formats. Find a good glue software that can help bind it all together where the applications otherwise have seams. For me, glue is LaunchBar and Typinator.
I don’t really understand this.
The workflow is:
Maintain database of references in bibliography database software (e.g. Bookends).
Write in Scrivener. When you need a reference, press Cmd-y in Scrivener, which takes you to Bookends, choose the relevant record in Bookends, press Cmd-y, which takes you back to where you were in Scrivener, with a temporary reference pasted in, looking like (e.g.) {Arregui, 2010, #97925}
When you have finished writing, export from Scrivener (by compiling, or exporting file) to rtf.
Scan the rtf file with Bookends, which will replace the temporary references in place with nicely formatted citations in the format you have chosen in Bookends, e.g. like this: (Arregui, 2010), and append a bibliography to the end of the rtf file with entries like this: Arregui, A. (2010). Detaching if-clauses from should. Natural language semantics, 18, 1–53. (Or however the bibliography style you have chosen formats them.)
What is this workflow leaving you to do manually that could be automated? (This is a sincere question – if you have a good idea, it’s likely that it could be implemented, given the incredible responsiveness to users of the respective developers of Scrivener and Bookends.)
Okay, thanks for your help. I exported my Mendeley bibliography to Bookends and used it to input my citations and the auto-generation of the reference list. It worked pretty well and was more seamless than my own fumbling through it. The citation shows as an endnote rather than "(Author, DATE), but I am sure there is a setting for that. I would want this format for drafting a research paper.
This is a big difference from Mendeley, which will only copy and paste the reference in text, not citations (although the feature is called “Copy Citation”).
One of the things that I like about Sente and Mendeley is the automatic importing of metadata. It looks like all the document information has to be added manually in Bookends. Is that right?
Given that, my workflow with Scrivener will be:
- DevonThink as the central repository for all my documents, this project and others.
- Add bibliographic information to BookEnds.
- Read documents in Skim, making notes and highlighting along the way. Export notes from Skim to specific Binder Folder in Scrivener. This way I can search just my annotations and highlighted material by searching “Binder selection only”.
- Copy file used for specific project to Scrivener (still don’t like having two copies). I really like the prospect of having a split screen with my reference document and draft on the same screen.
- Organise and Write in Scrivener
- Finish in Word 2011
I appreciate that there are specialist programs that are good at certain things. I can see how this integration works. Thanks for the responses.
Yes, you need to choose a bibliography format that produces that type of citations. I suggest Biblio>Default Format>APA 5th edition (That 's the format I used for the examples in my previous post.)
Absolutely not. There are several ways of getting information into Bookends. The best is if you have a pdf of a paper with a doi in the paper. In that case, if you drag the pdf onto the Bookends library list window, Bookends will offer to attach it to a new reference and find the reference information online. Rather magical.
Bookends can also pull in information from Google Scholar, Amazon, Pubmed and various other sources.
Then don’t copy the file into your Scrivener project, just drag it to the title bar of the second editor in Scrivener when you want to use it.
Workflow: open writing project in Scrivener. In Bookends, make a group of references that are relevant. When you want to see one of them in Scrivener, open the attachment in Bookends (Cmd-shift-o when the reference is highlighted) then drag the proxy icon at the top of the document in your pdf viewer (Preview or Skim or whatever) to the title bar of the secondary editor in Scrivener. Complicated to describe, but quick and easy to do.