References and Citations - what to use?

Hello everyone,

I’m about to embark upon a dissertation, and with the large amount of reading it looks like I’m going to have to do (hooray!), I started to think about the matter of managing all of these references.

I’ve heard things like BookEnds and BibDesk being mentioned, but I was wondering what programmes people used. What would you recommend?

Also, something else that has been puzzling me is exactly how I would use that kind of application. I suppose the first thing would be to enter items as I’m reading them, but when can it be useful when I come to write and want to enter a citation? Would it be possible to produce a bibliography at the end as well?

I suppose the other question would be about their integration into Scrivener. But is this actually important?

If you have any questions of clarification, please fire away!



IMHO, a reference manager is essential, not optional, if you are going to be using a large number of works that you wish to cite. I remember being in school and having to format all of the citations - a complete waste of time now that the computer can do it all for you.

I don’t have experience with BookEnds, but I do have experience with BibDesk and Sente. My research (more for keeping up with literature than actual publication at this point) involves the medical field, so it’s relatively easy for me to search the literature, and import the results of that search into either of those two programs. I never have to enter the bibliographic information into my citation manager, and never have to manually format the bibliography at the end.

I love to support open source software, and BibDesk is a great program that is under active development (perhaps not quite as active as Scrivener, but who can keep up that pace besides Keith… :slight_smile: It is where my references all end up (especially since I use MultiMarkdown when I do write, and it can be tied to BibTeX, which is the native format for BibDesk.

That said, for actually searching the literature, I’ve been very impressed with Sente. BibDesk can’t quite compare (yet) to Sente’s features in this regard - you can save multiple searches that are automatically run periodically. The results of those searches are saved to your computer, so when you’re on a plane at 30,000 feet, you can still go back and dig through your search results for additional literature. Sente is not free, but is worth the price (especialy with an academic discount if you qualify.)

My workflow is basically - search literature (and Library of Congress if desired) in Sente. Pull articles that seem especially relevant into BibDesk, where I have some scripts set up to automatically link to downloadable PDF versions of the articles when they are available. Export final collection to BibTeX format that can be used to automatically generate citations and bibliography in the final document.

Once you find a program like this that fit your work habits, you’ll never go back…

Thanks Fletcher, that’s very helpful! I’m currently looking into BibDesk; it seems to be very full-featured.

There are still a few questions that spring to mind, however. First, will BibDesk help me as I am writing to fill in citations? Second, do I need to have LaTeX installed for BibDesk to work correctly?

I guess really I’m asking: what would it look like for me to use BibDesk as I write in Scrivener?

Thanks again for your help so far!


I like LaTeX, and there are many reasons why I think it’s a great way to write professional looking documents. But, it’s a relatively complicated program, and not for everyone. I look at it like this: the learning curve for the features most people use is pretty quick, the benefit you get is the ability to focus on writing your document, and let the computer focus on formatting, generating a table of contents, bibliography, formatting citations, creating a glossary, and index if you desire (though the index takes some work on your part). One of the reasons I wrote MultiMarkdown was to make it possible to generate fairly complex LaTeX documents, without knowing much (if anything) about the LaTeX syntax.

That said, many users will not find it as easy as simply writing their document the old fashioned way - hand formatting everything in Word.

BibDesk has the ability to format a bibliography and export it to RTF, so that you could import it to Scrivener without LaTeX. By doing this, I believe you would lose the ability to have BibDesk automatically format the citations within your text, like it does when you use LaTeX/BibTeX. But that may not be a big deal for you. (BookEnds probably has some features like that as well - I am just not as familiar with it.)

As for filling in citations, as I mentioned BibDesk has some search features, but they are not as advanced as Sente (though this is an area under pretty active development, and it’s been a couple of versions since I really played with the search features.) It really depends on which database you want it to use to search for citations, and which program has the better support for that database.

Thanks again Fletcher!

I must say I’m genuinely intrigued by LaTeX and MMD, but I’m, to be honest, a complete novice to it, and wouldn’t have the first clue about how to use it, especially with Scrivener. Could you point me to any good introductions?



Among the three I liked the looks of Sente, but most of its internet search and auto-fill capabilities are of no use if you do research in the humanities and try to include some interesting stuff beside the mainstream. So I came up with BibTex /BibDesk, it has many features I do not need, but it is simply elegant, the text format is great, and it offers a lot for an unbeatable price.

Unfortunately, in my case I even had to abandon BibDesk because I need several options as regards the contents of output (mainly identical information in different scripts), which, as far as I see after all, is impossible with BibTex.

I agree with Fletcher that manual formatting is a waste of time – even when writing a short article. I wish one could insert tags in Scrivener and fill them with information from variable databases.


First, I would look at MultiMarkdown (an older version is built into Scrivener, but you can easily update to the newest version.)

Included in the zipfile is the XHTML and PDF versions of the user’s guide (the plain text source file is located in the Documentation Folder).

I also recommend looking at the Sample File: …

This zipfile contains the original Scrivener source document, as well as the plain text MMD export, the XHTML version, the LaTeX export, the RTF and RTFD versions, and the pdf generated from the LaTeX file. All of these were created automatically from the same source file (the scrivener document in this case, but you don’t need scrivener to use MMD).

It’s a good example of what it “looks like” to write a document in MMD, and an example of what the PDF can look like (you can totally customize the PDF output, but that’s relatively advanced and takes a while to learn enough LaTeX to do it properly…) I suspect most people aren’t interested in learning all about LaTeX just to be able to format their document, but like I said - MMD should do most of what the average user needs (citations, tables, images, ToC, even typesetting of mathematical equations.)

There should be enough about LaTeX on my site to at least give you a feel for it, but the official site is here:

That should be enough to get you started in deciding whether something like this would be useful to you, or more complex than you desire. But, I suspect that for longer works, the time you spend learning to use it (it’s pretty easy) is repaid several times over in time you save by not having to reformat everything and proofing for errors in citations, etc. But “your mileage may vary.”

That wasn’t my experience at all. My biggest problem was simply that my university (a medical university) didn’t subscribe to any humanities databases via the Z39.50 protocol (they only offered a web-based interface). I was briefly able to connect to one humanities database in education from Florida, but it has since closed off public access. But if you’re affiliated with an academic center that offers such a database, you can search for whatever you like.

I just don’t understand why it’s the bio/medical field that offers up one of it’s best databases to the public for free, but not other fields…

But this isn’t a limitation of Sente, it’s a limitation of the search resources available to the public.

I agree with you, you can search for whatever you like, but you will only find what’s in the databases. And there is so much that is not in there, at least in the humanities. I know that less than 20% of my dissertation citations can be found in the Library of Congress, and without these 80% it could not have been done. Same with many other topics, it is a matter of how deep one wants to get into a problem.

And I agree with you – less cynically :wink: – that it is strange that medicine provides such a good bases for bibliographical research. On the other hand, what is more important than medical research? I am glad research is so easily accessible from anywhere in the world, although I personally only make “use” of it if I visit a doctor…

And I agree with you that the limitations are limitations of the databases, not the programmes using the databases. The only shortcoming of these applications are that they only offer one entry per category, like author. I explained in another thread that I need at least 3 fields for entries of the author’s name alone. And I have to choose which one to use from article to article. Unfortunately, it seems to be an exotic problem, nobody wrote a reply on that post :cry:


I second fletcher’s notion concnerning Sente’s usefulness especially now that it supports Web of Science. Being a molecular biologist Pubmed is not the only place I need to look out for and WoS is definitely a big improvement. This Web of Science also includes Social Sciences Citation Index which may be of interest to those in the humanities.

That said, the humanities have very special requirements in the formatting which Sente is not designed to cater. I never quite understoood why there are so many different citation styles to begin with and frankly, some are over the top. There is a difference between styles omitting in-text citations or title of publications in the reference section, yes, but what is the big deal in using or not using periods in journal abbreviations or setting the journal’s name in italics? For journal articles we could easily (!!!) restrict ourselves to, say, 15 or so different styles of in-text citations and another 15 styles for the bibliography. That would do away with 99% of the utterly useless formatting madness and still fulfill every legitimate requirement. Maybe some people would even start paying attention to the content they are circulating…

rant mode off :confused: :slight_smile:


I don’t follow you here - BibDesk, for example, can store a long list of authors within the author field, and BibTeX can format this in your document to in a nearly infinite variety of ways (lead author, multiple authors, full name, last name with first initials, etc).

Perhaps you could give an example of why you need three separate fields for the author’s name?

I don’t follow you here - BibDesk, for example, can store a long list of authors within the author field, and BibTeX can format this in your document to in a nearly infinite variety of ways (lead author, multiple authors, full name, last name with first initials, etc).

Perhaps you could give an example of why you need three separate fields for the author’s name?

Hi Walafrid,

From my experience (and everyone’s is different) I would take Fletcher’s advice very seriously. I wish I had his brilliant Multimarkdown when I did my PhD.

Do a Search (at the top of this page) on key words such as PhD, dissertation, bibliography. There is some excellent advice on this forum - spread about a bit, but worth chasing down. I also posted a PhD template that is suitable for a PhD or Masters in the Social Sciences. You just need knock it into shape to suit your needs.

PS: You do realise you are completely nuts, don’t you?

Keep posting if you need help. The Scrivener College of Advanced Writing will help you. Lots of boffins from all sorts of fields here. All of them are generous to a fault.


I strongly agree, and that’s why I still use EndNote. Everyone loves to knock it, but it started years ago with Niles Software primarily for use in the humanities and social sciences. It allows for a wide variety of styles and output formats and is especially good at connecting with library databases and downloading citations. Yes, the interface is clumsy, but it works. And I’m fortunate to be able to buy a campus license for very few $$. I would prefer an iTunes-like interface, as with Sente, but its $90 educational license is too high.

I use Endnote 9, though to be honest, if I was just starting to need a bibliography program, I’m not sure I’d end up using it. :confused:

It is a program that - for me - lacks more than it gives on the whole, though that is strongly tempered by the huge hassle it would be to transfer all the info I’ve gathered over the years into a new program.

In the end, I may make that transition, no matter the hassle. The latest upgrade to Endnote 10 (or X as they call it) - $100/reg or $70 for a ‘special deal’ - seems to only have added one ‘big’ feature - PDF drag and drop!

If you can get a great deal like howarth, then perhaps it might be worth it to you, though.

Cheers for all the input and encouragement, everyone!

It’s good to know that other people here have had good experiences with things like LaTeX and MultiMarkDown (though I realise Fletcher’s biased as its developer!). I’m thinking increasingly that it will be the route I’m going to take, though it does feel strangely like there’ll be no way out once I commit: I hope you all stay around so I can ask questions later!

I’ve been playing around with BibDesk, and I think I will go with it for the bibliography manager. My choice was cemented by my university Library website being able to export into a BibTeX-compatible format, so no tiresome manual entry!

My plan now is to download a LaTeX package (MacTeX, I think–anyone had good/bad experiences?) and make sure I’m happy with all of that. Incidentally, Fletcher you may want to re-compile your Scrivener file example above (very helpful by the way!) because on opening it complains about being for an older version and opens blank, at least on my machine.

I should probably also clarify: I’m not doing a PhD dissertation, but an undergraduate dissertation in History. Still 15,000 words though! :open_mouth: So I’m not that nuts! (Maybe slightly).

Just to run this past anyone who’s done this Scrivener/BibDesk combo before, my plan is to write the footnotes something like this in Scrivener:

\cite{Bloggs1999hi}, p. 6

Is that the kind of idea? I’ll then run the export MMD to LaTeX option, open in TextMate, and run BibTeX. Phew. I’ll probably find out when I install LaTeX whether that’s completely silly or the right way.

Thanks again for all your generous input,


You can always export to RTF or Word, and salvage your words (if not the precise formatting), so you’re not too committed. In fact, I would argue that you are less committed than if you use a proprietary format, such as Word.

I used to use fink, but have since migrated to MacTeX, and have been quite happy.

Actually, what I would recommend is using the MMD syntax for citations; as things currently stand, your LaTeX code would be rendered useless by MMD.

[p. 6][#Bloggs199hi]

MMD will convert this to a form that is useful in XHTML, and then convert again to the proper LaTeX code as well. (As you get familiar with MMD, you’ll recognize this as a slight variant of the syntax used for links. The # designates it as a citation.

Read the User’s guide for information about how to link a MMD document to a bibtex file. Also, read it for information about the natbib package and \citep and \citet (two types of citations.) It should handle everything you need.

Ah, OK, I think it’s beginning to get clearer. (And I’m genuinely impressed by MMD!)

If I am writing away in Scrivener and I want to put in a footnote, and want to put in a reference for a work I’ve got in BibDesk, with citekey ‘CiteKey’ (original!), would this be right?

This is the sentence.[p. 5][#CiteKey]

What would I then need to do to turn the citekeys into actual citations?

Sorry if this is all simplistic stuff!


To turn the code into actual citations, you have two approaches:

  1. Save your bibliography in BibTeX format, and use MMD’s metadata syntax to set the .bib file:

When you export to LaTeX, and run it through the latex tool of choice, latex/bibtex will take care of it. My XSLT stylesheets include the support needed to include citations and a bibliography.

  1. If you want your references to show up in the XHTML version, you can manually append them to the end of the source file (see the above link as well). This works, but doesn’t offer the same features that the bibtex route offers. If you’re doing anything complicated, I highly recommend approach #1. If you just need some simple citations, this method works.

It would be great if you can help me there. I need the same information in at least 2 different options, but mostly there are more options needed:

Imagine a person is called “Gotô Teijirô”. His name can be written in Chinese chharacters, here they are: 後藤貞次郎. If writing an article in Japanese, this is enough, not if writig in an Western language, because we need transcriptions. There are different ways to transcribe the characters, and some publications need the transcription and the Chinese characters, some only the transcription.

Transcription: There are several ways which are preferred by several publications / persons: The transcription above is best, but some papers just want “Goto Teijiro” which hurts and is wrong, but they want it like that. Another correct transcription is Gotou Teijirou, and there is the transcription that the authour may have chosen and which has to be mentioned in some publications, it often looks like “Gotoh Teijiroh”. Of course, there are transcriptions which are basically correct but wrong in that special case like Gotô Sadajirô, which have to be chosen if the authour is mentioned under this name in another publication. All these are patterns, so I store the data in different pattern-columns and choose the column for each publication.

As for titles, there is the transcription problem and the translation problem: Some publications want a translation into another language, some only this translation, some the original title ( in Chinese characters and/or transcription) and a translation.

These are my basic problems, and I did not get around this in BibTex, to my great disappointment. If you know a solution, it is most welcome.

All the best,