Endnote vs …. well, everything else

Just before I handed in my thesis two things happened, which, up to then I had thought were PhD student urban myths:

  1. A whole journal came out full of articles that ‘scooped’ my thesis topic (gah!!)
  2. Endnote bugged out and turned all my 400 odd references into gibberish (instant coronary!!!)

My supervisor solved crisis number one with a single phone call. “It’s a good thing Inger,” he said cheerfully “Just point out in the introduction that the journal was published after you finished and this is evidence that the topic is hot“. Mischief managed (this strategy works really well by the way, even if you don’t have to employ it from desperation).

The Endnote problem was a doozy though.

Screen Shot 2013-07-11 at 4.05.02 PMNo students on the PhD floor at the University of Melbourne had experienced anything like it. Those who eyeballed my tattered thesis looked horrified. I could read their thoughts: Thank god this isn’t me! Believe me when I say this does not make you feel any calmer.

Frantic calls to the library resulted in pointers to some very helpful material, but that didn’t help. In the end, my mad skills of Google led me to an obscure Endnote support forum. On it was a post which detailed the problem I was having, but the posted answer didn’t work for me. I put a cry for help on the same forum and crossed my fingers. Over night a kind soul answered and fixed my problem.

Thank you internet!

But no thank you Endnote, you failed me in my hour of need. Up to that point I loved you, but ever since, no matter how often someone tells me you have lifted your game, you have been officially Dead To Me. I’d heard rumours there were better reference managers out there, so I got my thesis handed in and looked around for an alternative solution. These days I would just ask Twitter what my options were, but back then such research was more random. A photocopied flyer, which my friend Dr Scott Mayson picked up in a seminar room, led me to Mendeley.

I liked Mendeley instantly. It works in a similar way to iTunes in that you can make a ‘playlist’ for each topic and it’s social, so you can share your reference data with others. Your data is in the cloud, so no more data sticks and version control issues. The interface is lovely and clean which was an unexpected bonus (I think it’s a pity that the aesthetics of software design for functional programs doesn’t often get that kind of treatment). I spent a day or so transferring my data and LOVED the way it renamed all my PDFs in a consistent format at the press of a button.

Being a social sharing kind of person I put together a research education bibliograhy and linked it to the blog. I made an open Twitter literature list, added a few references and published it on the web. I woke up the next morning to find that many kindly souls had posted new references to it – instant literature searching! I was captivated and told all my friends about my new toy, trying to lure them away from the Endnote mothership.

But, like so many intense love affairs, the lustre eventually wore off and my eye began to wander. Once you have loved and lost a reference manager, it is so much easier to move on. I was transferring my writing practice into Scrivener at that point, and people on Twitter told me that cite while you write referencing worked better with Zotero.

Zotero is a project of the Roy Rosenzweig Center for History and New Media, and is funded by the Andrew W. Mellon Foundation, the Institute of Museum and Library Services, and the Alfred P. Sloan Foundation. The key feature of Zotero is the way it integrates with your Firefox web browser, plus Cloud, open source, sharing, automatic metadata scraping …oh – and free. What’s not to love?

Well I tried Zotero for a couple of months and, to be honest with you, I just couldn’t warm to it. After the aesthetic and functional design of Mendeley it felt hard to use and I never did quite work out how to synch it properly. It may well have had something to do with my migration to Mac from PC and the digital chaos that ensued, but I quickly tired of fighting with the interface. I know many people love it, but – not for me.

It seemed that Zotero was destined to be my rebound reference manager love affair. It was time to settle down and get married. All this moving around was hurting my paper kids. My digital life needed some order and routine so I turned again to Twitter with my wish list for a new reference manager. The wish list read:

  1. Easy to use interface
  2. Compatibility with Scrivener
  3. Good search functions and ability to keep notes
  4. The ability to auto-populate fields with meta-data from PDFs
  5. The Cloud. Baby.

. @vanderaj pointed out my wish list was unrealistic and suggested I try Papers2 for the Mac. While Zotero and Mendeley were free, Papers2 was $80, but there was a free trial for a month. It had everything I wanted but the Cloud, but that wasn’t a deal breaker because in the meantime I had rejigged the way my hardware worked.

Mr Thesiswhisperer is a professional software engineer. He watched me struggle with three computers (home, office and laptop) and decided the way I was working was inefficient (you have to love the way geeks think). He replaced all the computers with one slim, light 11 inch Mac Book air.

Instead of maintaining and synching data on multiple computers and remote servers, I now cart all my data with me, which would be dangerous if Mr Thesis Whisperer had not also installed Time Machine. When I turn on my laptop inside my house, Time Machine finds me and slurps up all my latest work. So fantastic – we live in the future right?

Anyway, Papers2 turned out to have a great search function, combined with note taking and highlighting capacities. It is wonderful at scraping meta data from PDFS and populating fields like author and publisher. Often these are not properly done in the first place (honestly – I really do wonder what we pay those journal publishers for). If Papers2 doesn’t get the fields quite right you can ask it to search the web and find a match.

Thanks to @jasondowns and @scottmayson I have discovered other cool features such as the ability to set up a proxy and search databases like Google scholar from within the interface, which enables me to import from the web, seamlessly, with one click.

In other words, I’m happy with Papers2 for most of what I do (but I still use Mendeley to compile libraries on to share on the web). I think this story demonstrates how the choice of reference manager is deeply personal and contingent on a whole lot of factors. Sometimes I yearn for other features, but the more I get to know Papers2, the more I appreciate its trusty and efficient design. Deep lasting love is always like that, at least so I’ve found.

That’s my story – what’s yours? Did you stick with your first reference manager or kiss a lot of frogs until the right software came along? Perhaps you have some other, totally radical solution for keeping your references in order? Would love to hear your stories in the comments.

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212 thoughts on “Endnote vs …. well, everything else

  1. I use Zotero exclusively. It’s fully featured, I love the chrome addon, and all that stuff that the competitors have. But what it really comes down to is the fact that it’s open source. If I find a problem with Zotero, or something I don’t like, I just look at the source code. I’ve not had to do this with the main program so far – it just works. But I’ve hacked on the formatters and exporters and I can make it do whatever I want. Closed apps can’t compete.

  2. Had over 1000 references in my thesis and zotero never let me down. Also used it for all my publications and the only issue I had with that was that it sometimes took a while to find a similar reference style to a journal that is not on the list. However, new styles are being added all the time so it has become less of an issue.

  3. I prefer LaTeX for all writting. I find LaTeX to be easier to typeset than anything else I have tried, especially math equations. Hence I prefer JabRef, which is BiBTeX manager. It is cross platform and can do a lot of tricks with .bib files. I keep everything in dropbox (or any other cloud service) to keep things synced.

    I am also very comfortable with version control systems. All my papers, thesis and projects are managed by GIT/SVN – It really does help to improve the text/code by easy comparison with previous versions.

    By the way, I find it ridiculous and very non-geeky to replace all your computers by a mac-book air just to solve a relatively easy problem of syncing data across devices, especially for a graduate student. (Most of graduate students run low on economic side given the ‘peanut’ amount of stipend they get).

    • Well, since you bring it up. It was simpler and cheaper to have a single, easy to cart around Mac and back it up properly than buy 3 computers (one for office, one for home and one for the road). Managing data *sounds* ok until you consider that not all internet connections are the same. At uni it is fine, at our new house the internet pipe is not so lovely. If you had walked a mile in my shoes you would have understood the decision I’m sure 🙂

    • Having heard many horror stories about how ‘Word ate my thesis’ and the like, I totally agree that the LaTex/BibTex solution is much more robust and reliable, especially when used in combination with a version control system, such as GIT or SVN. However, LaTex is not user friendly because I think it can be characterized as ‘programming for authors’ and not everyone has the basic skills to be comfortable with this sort of format.
      On the other hand, we are seeing the inclusion of programming elements in PhDs across the Science/Engineering domains and into the other disciplines, such as Design and Arts. As an example, one organization, software-carpentry.org, has produced a free program of lessons that introduce students to programming and software engineering skills such as: version control, data manipulation, and scripting. Do you think they should include LaTeX for non-scientist?

      • LaTex just doesn’t feel user friendly to me. I notice that everyone who recommends it is in science / engineering – maybe they have some cognitive plug in that I lack 🙂

      • LyX (http://www.lyx.org/) is a graphic interface for TeX/LaTeX which means that you don’t need sophisticated programming skills to use LaTeX anymore. Having said that, it’s still takes a little time to learn LyX.

      • I have worked extensively with both LaTeX and MS Word (and a number of other tools using Markup resp. WYSIWYG).

        Frankly, LaTeX wins hands down and it is a mystery to me how people can consider it user unfriendly. Yes, the learning threshold is higher, but in return I actually get what I asked for, mysterious errors do not happen, I can use SVN et co. with ease, diffing is an easy task, I spend more time on content and less on layout and formatting, if I want to change layout/formatting I alter a definition in one place, … Word and its ilk, on the other hand, has had me just short of throwing my computer out the window on a number of occasions.

        (As a general observation, user-friendliness is not a matter of usability for beginners—it is matter of usability. Beginners should be given due consideration—but so should intermediate and advanced users.)

        Most notably, if you are serious about editing then it is vital to have a proper separation of content and display of content, which WYSIWIG lacks and which makes it fundamentally flawed. Excel (and similar spread-sheet tools) are even worse. Here a three-fold division should be present, but is invariably missing: input data, calculated data, and display of data.

      • It’s definitely an engineer thing but i love LaTex + GIT. I can’t imagine myself ever using MS-Word or similar for anything long or important.

        I’ve just started a PhD and for now I’m using Mendeley because:
        – It’s free
        – The Mac app is quite friendly
        – It’s not bad at pulling the meta data from pdfs
        – It manages my pdfs (and can rename, folder etc.)
        – Exports to bibtex
        – Cloud hosted and has mobile apps (so at home i can take my iPad to the couch for some relaxed reading

        The only thing i would like is custom fields, i’m not sure if other products do this. But for now tags are good enough. I haven’t tried the social features but they sound interesting.

    • Endnote can go weird when working with large word documents in lots of successive updates… like a thesis draft. This happened to me at the end of my PhD, and all the references moved position in the text. The answer turned out to be pretty simple (after I got over the heart attack). Basically if you keep endnote citations ‘unformatted’ until the very end, and then format them once your drafting and re-editing is done, all should go smoothly. It seems like repeated drafts of large word docs gives endnote a funny turn, especially if the citations are formatted and you’re using master document features. (It also is a really good advertisement for keeping regular backups!) For the record, I still use endnote (it has over 2500 things in it so I’m not starting again!) but I always keep an ‘unformatted’ copy of the recent draft to hand even when sharing formatted versions with co-authors etc.

      • Thanks for the explanation – and great to have a solution. Wish I’d known that at the time! But you’d THINK they would design it specifically for that situation right? I’d better not say any more 🙂

      • As an ardent EndNote supporter I would like to point out that at least some of these problems may actually be caused by using Word’s notoriously unstable Master Document features.

        I’ve used EndNote across multiple computers, with different authors, and always used auto-formatting. The only issue I’ve ever had was that towards the end of my thesis the citation formatting was taking ages to update and causing lag (when I needed to update lots in a row). I had formatted citations turned on for my thesis for every single draft (and I have lots of “final final really this is the final version.doc”) and never had any issues. Although, obviously, having issues is so traumatic for the people they happen to I can understand why you’d never trust some things again.

      • I never used the master documents feature because I was warned about it, but it still happened. I suspect, after reading some of these wonderful comments (thanks everyone!) that my word doc was just too long.

      • When paid software can take a ‘funny turn’ during a critical function, that’s a pretty good reason not to use it. They’re making a lot of money, they should be able to afford decent software engineers.

      • You also need to remember to work with unformatted citations when merging documents together (such as moving thesis chapters together into one document)

      • Truth is that probably it is not wise to write a whole thesis in one Word doc. I try not to use Word for anything if I can help it. At best I would use one Word doc per chapter. I don’t understand why so many still don’t do this. I had a colleague recently who still has PhD students who just sits there open mouthed when he sees this.

      • I think we talked about this on twitter but I like Endnote as a reference manager but never really use it integrated with word because it was so buggy when I did try this years ago (like 8 years ago so maybe it is better). To be honest it might be my research area or just the habits I have developed but I don’t feel the need for a program to integrate with my document and create my bibliography for me. I just write references them as I go and just maintain a working bibliography separately as I like to be able to quickly see my bibliography.
        That said I have used Zotero on and off and am using it now for a collaborative project, I do like the way it works well with webpages and news and images. And someone just showed me an app for Zotero where you can use your phone to scan barcodes and it uploads all the bibliographic info into Zotero. Also ever since moving to mac I am less fond of the endnote interface.
        I found Mendeley wasn’t very good for my particular research area, hardly anyone else was using it and it didn’t ‘read’ a lot of the databases I used.
        I might have a play with the Papers2 free trial.

      • Years later, I’m writing my first academic paper in decades. Thesis Whisperer, I am finding your original post with cautionary tale and your experience with different reference managers, AND these comments by others, extremely helpful as I try to choose one. Having used it at a past technical writing job that was a UNIX shop, I would not recommend LaTeX for anyone who doesn’t want to have to learn to program. It’s a great tool – for people who are happy being geeks and willing to invest the time. And Microsoft Word has always been dangerous to use for really long documents. I remember well inheriting an entire technical manual that someone had unwisely put into a single Word document, and seeing the “blue screen of death,” or a big red X where an illustration included by reference was supposed to appear, at 3 AM before a deadline, because Word had apparently exceeded its maximum internal size and addressing-space limits, and so spazzed out. Word started life as a little program envisioned for business letters and brochures. It was not designed with very large documents in mind. Adobe FrameMaker, the unstructured version, was excellent four or five years ago, and does have a learning curve, but will never, ever bite you. I don’t know if it now integrates with reference manager tools. Unfortunately, FrameMaker is expensive.
        I got out of tech writing and now work at a solar installer. I am now on the hunt for which document creation tool to “marry” for my career as a mid-life grad student.

  4. I use Mendeley pretty much because of the iTunes resemblance. Plus, I get to download tons of papers to a single computer at work and I have -most of- them available when I get home (choosing which ‘playlist’ to sync depends on what I’m currently working on). The freeware part was also a huge reason for choosing it, I had no money when I started this gig.
    Some people just can’t quit endnote and I don’t really understand why. The only thing I like about payed software is that you have someone to turn to or yell at, which leads me to the following: Why did you have to find an obscure forum when you could have just called customer support or something similar?
    In short: For me its Mendeley all the way!
    Best wishes from Mexico!

    • I tried customer support via my library, which should have worked. I was going to ring Endnote directly the next morning, but since the forum person fixed it overnight I didn’t have to 🙂

      • Hi – I’m a librarians, and I’ve spent a lot of time assisting people with EndNote problems similar to yours. As the document gets larger, everything gets a little less stable. As Kathleen says, unformatted citations are better for larger documents – you don’t have EndNote and your word processor chattering in the background and slowing everything down. Another huge tip is to only ever have a single Library (otherwise the formatting of the citations can get mixed up), and deduplicate your Library before starting to enter citations into your word processor. I’m sorry you had such a bad experience with EndNote, but by and large, I think that it’s still pretty good, and it’s busy looking over its shoulder at Mendeley and Zotero too…. means newer features.

  5. I fell in love with Zotero in 2006 and instantly became an early adopter. I used it with the “cloud” backup which came in handy when my laptop was stolen *twice*. Each time, Zotero had my back and all of my research notes backed up to the cloud. Contrary to Thesiswhisperer’s concept of a single computer, I have Zotero working on all four (or five) of my computers and a thumb drive and they all sync to each other. It is beautiful. By the time I was completing my PhD dissertation, I had all of my references in one file of Zotero. I also used Zotero for the final copies of my dissertation. I literally compiled my bibliography in 15 minutes. It was awesome.

    • Oh sorry – didn’t mean to imply that I couldn’t have managed multiple computers with it. Just that in the Mac / PC change over I lost the library twice and lost interest in fighting to get it to work. I know it works wonderfully for many people, which is why I often recommend it as a ‘go to’ free alternative.

      • Than you, Laura,The pre-session testing and cocuinimatmon comes from experience, my co-workers and I are often on the receiving end of a call from someone who wants to train in one of the labs we manage. They’ve left things to the day before to check that things will work, and we don’t have the version of Office they need, or something similar. We try to do our best to rush changes, but sometimes I think we feed their expectations doing so; the same people tend to do it over and over again.I was new to Mendeley, so I haven’t kicked the tires much on the social aspects. I wish there was a way to contact the other people who read the same documents that you have. Or a research collaboration match-making tool. Maybe they will come. Maybe they are there, but I missed them.

      • Can you tell me what is meant by keeping “endnote citations ‘unformatted’ until the very end, and then format them once your drafting and re-editing is done.”? I see that a lot in these posts, and I’m not sure what that means. I am considering End Note 7, but with all the comments, hesitant to plunk down the $

  6. I’ve used Refworks, which is clunky but effective, but when I changed unis the new one had no Refworks account. I turned to Mendeley because it was the easiest to use of the freebies. It has glitches…like chapters with lots of references go slowly unless you use IEEE and change to Harvard at the end. Also, it has a limited online free account size but this can be overcome if you only synch the titles (not PDFs) with the online account.
    Their customer service is usually good, and the support page has loads of topics to browse. For a freebie, it’s immense: library and citation manager all in one.

  7. I used Zotero but didn’t like it much. I can’t say why, just didn’t work out for me. I’m using Sente now and I LOVE it. I have the iPad app so I read my articles on my iPad (which is automagically synched into my laptop and lab computer), and I can have all my notes and all of my references on the go (e.g., thesis defence, conferences). I can use DOI to automatically import a citation. I don’t use the cite-in option though, because I find it very annoying (tried it a few times, but now I just look the citation up and type it in). What I like about Sente is that it uses tags, so one article can be tagged with two different “collection tags” (e.g., theory review and executive functions) and I find that very useful. I also like the status option, and I have built a “reading list” using the “To be read” status. In short, it really fits my flow which is what’s important 🙂

    • I love Sente too. I just started with it a month or so ago but I love the search functions and the way it keeps records of where data was found (along with webpages). Also, it was important to me to be able to use it on my ipad since that is what I tend to take to the library. Sente works really well on the ipad and uses the cloud to update so all my data is on my computer too. Also it works with Pages, which I quite like.

    • But you can have label/tag to multiple collections in both Mendeley and endnote.
      As a matter of fact recently though I am having a nightmare of a time due to endnote x7 budging out for each library declaring library in multiple use(liar), it got corrupted.
      Mendeley popping up messages to send a love letter to support@mend****….I tried docear, zotero a lil but that I have not still settled down with any one.
      Still single and looking …….

  8. Just a small nit, but Zotero is not “made by the clever folks at Mozilla” and is, in fact, in no way associated with Mozilla (besides using Mozilla’s XUL Framework at its core). From zotero.org “Zotero is a project of the Roy Rosenzweig Center for History and New Media, and is funded by the Andrew W. Mellon Foundation, the Institute of Museum and Library Services, and the Alfred P. Sloan Foundation.”

  9. I had also used and loved Endnote for years until it went all nasty on me a month before my Masters thesis was due. IT somehow also seemed to corrupt ( or maybe it was an evil co-incidence) my Microsoft Word. I cried a lot!
    I had to delete my Office software and reinstall and then manually check and correct all the formatting problems in the document as well as the references – in-text and reference list. No-one I spoke to seemed to know what had happened or how to fix it but I did get lots of anecdotes about friends of friends that this had happened to. I havened had the guts to use it since and manually reference while I play with other tools. Thanks for the list. There’s a few I haven’t tried..

  10. I started out with Zotero – I like it, but had to abandon it because it was not as portable as I needed it to be. And as you pointed out, it could be a bit clumsy. I then moved on to Sente which works great with Scrivener, syncs instantly across all of my devices (I’m using Mac) and handles everything I can throw at it rather well.

  11. Thank you for your story and alternatives. Your own experiences of both loss and learning will help many on a similar study journey

  12. I have Papers2 on my laptop (mac) and in the office computer (windows), and despite a few problems, it works better than any other software. You can synchronise your papers among devices in the cloud using DropBox. I also use Papers2 on my iPad, and it´s very useful to show some papers to my supervisor in our meetings

  13. I have to say, after having tried most of the aforementioned reference managers I just keep going back to EndNote. I haven’t tried Papers2 and it may be time for another round of testing! Thanks.

  14. Interesting read – thanks both for article & comments. I am using qiqqa (after being utterly disappointed by endnote). Qiqqa’s multiple tagging, sorting/linking/analysing, bib search, annotate, etc seem to work well for me with access across multiple computers via sync. Refs import to word (or there is a cite while you write option but I have found it not so quick & easy). Does anyone know how this compares to the others? Thanks & happy lit reviewing!

  15. I am currently using Endnote as a library, to export into a textfile to be converted into Bibtex. A few months ago, I was on the verge of changing to a new reference manager, but decided against it as time is running out. Endnote has been quite disappointing so far due to 2 reasons!
    1. My library has corrupted so many times. I have to save several backup copies now.
    2. It is just not the best reference manager to use with Bibtex. I think JabRef might be better. But, I realised that way too late.

    Definitely switching to a new reference manager next!

  16. I use BibDesk on the Mac ( http://bibdesk.sourceforge.net/ ) which is free & open source. It works well for LaTeX/LyX (although I have formatting issues with the ref. list, but that’s to do with LaTeX templates, not BibDesk)

    It can also generate reference lists for whatever else you want to use (not as intuitively as with LaTeX, mind), works will with Skim (a really good PDF reader on the Mac with academic reading in mind), and has iTunesy Smart Folders and QuickLook for viewing documents. It also files away your papers, iTunes style, so you don’t have to deal with unsorted folders (I augment this by having a Folder Action to make an “inbox” for papers, so they open in Skim, then when I finish reading, drag them into BibDesk, which moves them to its filing system…)

  17. Oh, how timely a post for me! I am submitting in early October and had a highlight with EndNote several weeks ago. I moved to RefWorks as I could get a free account through uni and it would load my EN bibliography automatically. Fantastic until today when I suddenly had only one reference in my library. I burst into tears in tge library (as it happens, I had a backup in Dropbox and only lost a few refs, but still…)

    I guess the point f my long boring story is that for a split second I considered going back to ‘naked bibliographying’ but I don’t think it’s ever worth it. (I do like the sound of the social-aspect of Mendely, but honestly I like NetWorks way more than I thought I would. Not sure showing works with Scrivener though…)

  18. Hi, thanks for this post. It’s timely for me. I’m at a bit of a crossroads with this stuff. I’m almost half way through my PhD, using a PC at Uni and a Macbook Pro at home. I’ve got Endnote for Mac version 5 on my Mac at home, but of course I can’t use it at Uni. (I was actually advised against doing this by the Endnote training people at my uni. They said it would be a “world of pain”.) Anyway I haven’t used Endnote in any of my writing yet, I’m just using it as a repository (not a “suppository” lol) for all my articles. Actually I’m a bit scared about embarking on writing my thesis with Endnote for Mac when I can’t use it on my Uni PC. Does anyone have any advice for me? I believe Endnote Web isn’t the answer because it’s not fancy enough for a PhD sized thesis. As you can probably tell I’m not particularly tech savvy and my hubby is not a computer engineer! Thanks 🙂

    • For years, I used Endnote. I recently moved to the Mac, and switched to Bookends. Bookends integrates with almost all the authoring tools other their including MS Word, Mellel, DevonThink and so on. It’s really helped in keeping related PDFs in order as well.

    • Hi Lee
      I’m not sure what version of EndNote you’re using, the last 2 versions X6 & X7 allow you to sync your EndNote Library on your desktop to EndNote Web and subsequently sync it to another computer with EndNote on it. Alternatively, you can run your EndNote library from an external harddrive(making sure you have a backup somewhere just in case) and move your library from computer to computer that way.
      I’ve helped people( I work in a Uni Library) on Mac’s with problems in their documents, opening their documents on my PC without any problems. So you should be ok to move your document from one to the other.

  19. I used Zotero on my MA, using the Libreoffice word processor. There was no problems at all, and the benefit of open source is an active and visible forum for any problems that do arise.

    Despite the fantastic feature that automatically creates entries from library database pages, I did find the Firefox plugin a little clunky to use, but now there is a stand-alone Zotero that creates a better user experience.

  20. I second the LaTeX + BibTeX under version control suggestion.
    I do exactly the same (these days mostly under Git) and that works really well.

    Some of my students have also used, after I showed them it was pretty cool, WriteLaTeX: https://www.writelatex.com/
    Essentially LaTeX in the cloud with the the ability to invite other people to collaborate on your docs (more useful for papers, but sometimes I annotate my students’ chapters in there).
    It also allows to save checkpoints for the document (very rudimentary backup/VCS solution)..

  21. thank you so much for this post! I am just about to start my PhD and I’ve been trying to learn Endnote as it has been recommended by our library in school. I’ll go back to using Mendeley since I’m quite scared of anything buggy happening in the end. Citing can be a real nightmare. @_@

  22. I currently still use Endnote, even after trying Mendeley and all the rest. Mostly, it’s because much of my primary source research uses Arabic, and I haven’t been happy with the integration (or lack of!) for non-Western alphabet languages. Many of the PDF files that I have are also scanned Arabic texts, and as OCR for Arabic is in its infancy, the highlighting etc. features found in Mendeley simply doesn’t work as they are treated as images rather than text.

    I’ve found that keeping a version of my chapter/file as unformatted citations is helpful, and also making a version where everything is “converted to plain text” (i.e. from within the Endnote menu, so that everything is formatted and no Endnote required). The latter is especially useful for sending to supervisors/readers who don’t have Endnote. I’ve also exported my entire bibliography list as RTF, and XML for backup, so hopefully have things mostly covered!

  23. I loved Endnote when I was writing my thesis. I worked on each chapter separately, occasionally formatting the citations but mostly working with them unformatted. I only combining the documents once I’d completely finished the thesis, and then formatted the citations – having saved a copy first in two places! I had no problems, except a couple of references that went wonky at the end, but they were easily fixed. I think, as people have said, that Endnote doesn’t play well with huge documents and repeated saving, and it’s better for Word as well. Another trick with Word is to use SaveAs at least once a week – it seems to cut down the problems with huge files crashing.

    But now I have time I want to investigate Papers2, which my partner is very happy with. But it is hard to change if you don’t have a really compelling reason.

  24. Thanks all. Real interesting and helpful. Like many others, just embarking on phd. Used to Endnote but wary of its crashes. Like the sound of the iPad apps.. Seems as though its either Papers2 or Sente!
    Looking forward to reading others experiences!

  25. I’m with galpod. I tried endnote and papers, but I’m a Sente fan. The tagging is awesome, and the latest version has really lifted its game in the syncing between ipad and my two Macs. I love the sharing aspect of Mendeley, but the ability to read, highlight and make notes on papers on my ipad sealed the deal for me with Sente.

  26. I used Mendeley exclusively for my honours thesis last year and it was perfect – loved it to bits. Now, however, I am finding more and more things that I do not like about it. Most of these have been put forward as suggestions for future updates on the Mendeley website but progress has been incredibly slow and there has not been (to my knowledge) a major update for a several months, at least. The ability to search for a paper and then order the papers found by year, author, journal, etc. would be great, as well as the ability to ‘undo’ highlighted passages within documents. This lack of basic features is frustrating on a daily basis. If Mendeley doesn’t lift its game soon I’m afraid that we will have to break-up 😦

  27. 🙂 The Papers for iPad is definitely worth trying. Everything you mark up on the iPad is then synced back to your main library. It’s a manual sync across your wifi network, but still nifty. Sharing PDFs with other @papersapp users is simple too. So far it works for me, and it works well. I’m SOOOOOooooo looking forward to sending my EndNote to burn.in.Hell. I’ll use apptrap to make sure that when EndNote is deleted off my mac that all its evilness is exorcised.

  28. I am using Endnote for my thesis. I will eventually use the Word masterdoc feature, but at the moment I am just doing each chapter as an independent document. I occasionally have problems with reference formatting and am glad to see the info about using the references unformatted because the docs I have problems with are ones that I’ve worked over about a bajillion times (I am studying part time, so have been doing this a while and people keep *writng* stuff). I have tried Zotero, but didn’t like it as much as Endnote and I have edited five or six doctoral theses for other people and found that Endnote was fine for all of them. I think it is much better than it was (I think I started using Endnote 4 or 5) and I don’t have the energy to start again at this stage. I have certainly never had a crash. I back up to the cloud.

  29. I had a very similar experience with Endnote. I was handing in the draft of my PhD proposal and after printing copies of the roughly 40 page document I realised that some references had swapped places. Nothing looked obviously wrong at first glance, and yet there were glaring errors where work of one author was now referenced to another (not the right author) person! I believe in printing hard copies at regular intervals (and backing up to all sorts of places) so I was able to manually go through each page and flag the Endnote stuff-ups to change them back to the correct reference.

    I agree with some of the comments here that Word may be the problem. I lost numerous section in Word while doing my Masters when the document would just freeze, refuse to save and then on reboot have thrown me back a few hours. I believe the problem has something to do with the size of the document, so my PhD thesis is being written in seperate Word “chapters” to try and keep some seperation.

    Regardless to say, I will never use Endnote again, and I admire you being willing to use any of these softwares. Im simply too paranoid now to risk it happening again, and instead will be doing it the old fashioned way. These sofwares only save time if they dont crash, and as I now feel that I would have tocheck as carefully as I would for the manual way of doing things I am rather just doing it the “old” way. I make sure to include each reference as I use it, I include page numbers (do this wether your referencing style calls for it or not so that dealing with queries is easier) and lable pdf/research files “author_date_fulltitle. – its long but it works.”

    Its all a hack, but personally I feel it’s a much smaller stress that going through a crashed referencing program again…this time on a larger document!

  30. Sente is really excellent. I’ve also tried Endnote and Mendeley, but the iPad integration of Sente with the desktop works really well. You can attach all your papers at the desktop, and read them on the go on the iPad version. All your notes, tags, etc will automatically be kept in sync across both.
    Only potential disadvantages are that it costs and is Mac only.

  31. Word’s master doc feature is very, very RAM hungry when you are working with a document that is as long as your average PhD thesis. I am actually now re-thinking using it. I will see what happens if I just paste all my chapters into the one document (with unformatted references) then reformat.

    • Master docs was a real mess for me. Basically it shut down the computer it made everything so slow. In the end i had to cut and paste it all together, which worked better, although Endnote still had a wobble at the end.

  32. Good story. Thank you!
    I also have been through this search for good reference meanger software and ended up with Mendeley. Works for me, so far. However, I agree, there are some shortcommings. What I already knew of, but never tried, is this social aspect and sharing functionality. For the upcoming lectures I will definitely try this. Might improve my score with the students!

  33. I am a long time Zotero user, but have given up on the cite as you go features of any program. So i keep a record of my citations (imported using the Chrome importer), make notes, and attach PDFs. Then I copy my citations into a footnote and check that they are correct (usually not the case) and edit them.

    This allows for a neat trick I learned of late (only useful for those w/ footnote styles):

    Select all footnotes and copy into a new document.

    Delete everything that isn’t a ref, and check for errors.

    Use the sort feature in word under the Home>Paragraph section.

    Bingo! references are sorted alphabetically, and you get to check for errors a the same time.

    • Have you reported the incorrect footnote citation on Zotero forums? We’d be interested in improving it if possible.

      • Hi Aurimas,

        The problem isn’t actually that Zotero is causing problems, but that the original metadata for the sources is often incorrect. It also spectacularly fails to properly cite things like chapters in edited volumes from time to time. I’d say that most citations have at least one small error in their metadata when taken from the web, so I like to check.

    • Can’t reply to your reply (nested too deep), but those are the sorts of errors that we would love to hear about. We always try to fix import errors. Often the metadata is not correct on the websites, so there is not much we can do. But there are cases where Zotero can be improved (and these improvements go live instantly). So please do report.

      Regarding improper citations, those are even more important for us to be aware of and fix, because users are les likely to catch these errors and they affect a large amount of citation managers. Above I commented that Papers2, Mendeley, Zotero, and many others use the same styles, so this would affect most software packages.

      Zotero strives to be as seamless as possible. If you find yourself doing this much work to add citations, there’s certainly something that needs fixing.

  34. I used Papers 2 for my thesis and it was also one of the reason I switched to Mac from Windows (there was no Windows version at that time). I can not say enough how much I hate Endnote. Now I’m using Mendeley as they also have Android version to sync with.

    Recently I use Readcube for literature research. Its recommendation and search engine is very good in my opinion. So bad there is no sync or cite functions (as I use both Mac and PC). The library management function is not very good and the software in general is not “native” as they use Adobe Air, so its UI is also a bit funny.

  35. Hello there,

    I’m a bit of a ‘lurker’ on this blog as most of the articles are more relevant to current or recently graduated research students. I’m about to enroll for PhD in mid-September but I love reading your blog already so thank you!

    This article is the first that has really struck me ‘where I am at’. I am about to enroll and with the fervour of a schoolchild picking out a new pencil case I am researching which software to use to organize my ideas, writing and citations.

    I’m currently rocking a Sony Viao laptop that came pre-loaded with Evernote which I can use to collect ideas. Outside of the digital realm I use a lovely fountain pen and moleskin notebook to collect my ideas with the added bonus that I look like a dandy fop.

    I figure that there is no match for Scrivener so my writing tools are taken care of. However, I am stuck on which reference manager to use. Principally, I am looking for something which is good at picking up meta-data and integrates quite will with Scrivener. I’m going to stop there because this is starting to sound like an ad on a dating website.

    ‘Young academic type seeks reference manager for no strings fun. Must be clean, discreet and have a good sense of humour.’


  36. I had a very similar issue with Mendeley that you had with Endnote. After adding about the 10th reference, my document got totally bloated. Unfortunately, this was during my comprehensive exams, so a rather stressful time. Fortunately, I had a backup – Bookends. I’ve since discovered that Bookends is now doing a lot of what Mendeley does. I’ve also found that when I have an issue, I post to the forum or email support and usually get a response within hours – and the response is often from the developer! So, when Microsoft put out an update that broke Bookends, I sent an email and had a work around the same day. When I contacted Mendeley about the problem I was having, they thanked me for reporting it and said they might be able to get to it within 2 months! So, over the last 2 years, I’ve had a consistent level of fast support from Bookends – makes it worthwhile to me. Especially now that I know I can drag and drop PDFs to add them to the system.

  37. I did my masters dissertation in Menderly, and I loved the interface. However, I was always nervous about the fact that it was a closed-source system and that there was no straightforward way to extract all of the notes and annotations that I had made.

    This uneasiness was magnified when Menderley was bought by Elsivier, and since this timing coincided with the start of my PhD, I switched to Zotero – since it’s open source, I know that I will never be “locked in”. Also, it supports non-Apple tablets much better than Mendeley ever did – now I put the papers that I want to read on my tablet, read them and annotate them on the tablet, and pull them straight back into Zotero.

  38. Mendeley is my life saver. It’s perfect for compiling bibliographies in Word, but my favourite part is how easy it is to read, highlight and annotate pdfs. I do most of my reading through the Mendeley interface now. I’ve tried all the programs you did, Inger, and Mendeley definitely won.
    It is very satisfying to finally, publicly, admit… I hate Endnote!

  39. The first I have used is refworks*. Easy and you can access your ref anywhere through the internet. I faced some problems as it conflicts with antiviruses in the computer but helpline are useful and they solve all your problems. I recommend it to everybody.

  40. Awesome post! 🙂 I have tried just about every reference/bibliography manager, on both PC and Mac: Endnote, Sente, Zotero, DEVONthink, etc., etc., etc. I have settled upon Mendeley+Citavi (PC-only for now but a web-based version is in development). For some reason, the metadata issues in Zotero got me and the Zotero interface did not feel like “home.” Endnote just always felt off-putting. Note-taking in Endnote was cumbersome (I heard it’s better now?). But in Mendeley, the “foldering,” and tagging and keywording and annotating and highlighting are phenomenal and leave your original PDF clean. Citavi adds knowledge-management and facilitates writing in a way that does no other (I abandoned Mac before Papers, though, so Papers may be great here, too). Knowledge management allows me to research, read, note-take, and analytic memo-making with the long term in mind. Citavi works easily with Google Scholar and Mendeley (I import BibTex from Google Scholar into Citavi). Citavi works easily with Scrivener, or any word processor, really. I can never thank the person enough who mentioned Citavi to me. I fell in love with Citavi, introduced Mendeley and Citavi, and have abandoned all others (smile). I annotate and note-take in Mendeley, copy the important information to Citavi, and copy from Citavi to my word processor. Citation info tags along when I copy from Citavi to the word processor, and later Citavi magically formats it all correctly and builds a works cited based on citations. AWESOME! If in Citavi I click on the keyword “methodology,” then every quote, note, paraphrase, etc. that I’ve EVER taken about methodology will populate to one screen with PERFECT citation information. PRICELESS!

  41. Thanks for this, Inger. The only reason I used Endnote was because the uni ‘supported’ it. When I, too, lost over 400 references noone at the uni knew why, could help me or really gave a rip…. so I am so happy to follow your advice and stray 🙂

  42. I did my references manually. My reference manager was a Word document filled with references, abstracts, and hyperlinks. The document was backed up on floppy disks, CDs, and hard drives. Foolproof! 😀 I never did figure out how to use EndNote….

    • I was just starting to think I was the only person in the universe who did their PhD with manual references (well, in the last 5 years, anyway)! I only used Word’s footnote function, then manually typed, checked, edited and rechecked every single footnote. Loved the fact I knew it wouldn’t crash – and I still finished on time and perfectly sane. Well, moderately sane. Sane enough. Apart from those few nights when I dreamt about footnotes.

  43. I don’t recommend ever using word in long doc fom and endnote. What can work well is to do each chapter with live citations from endnote then break the hyperlinks before putting your thesis together in complete form. This makes it far more stable. That way you can just export however many references into separate chapter that becomes the bibliography and you haven’t missed any. I’ve found it works a treat. You can still use the master doc format but just keep each chapter separate.
    I still use endnote and word and share project bibliographies with many on share drive and Dropbox. Seems to work just fine.
    Having just spent a day trying to transform a LaTex doc into word to submit to a journal, I am never going there….

  44. Thanks for a great post and a lively comment thread. I’ve started to notice the Endnote gremlins at work myself, even in 10 page documents. They’ve been substituting correct citations with other citations in my library and when corrected, they occasionally switch them back! Let’s just say I was lucky I could correct them from memory. Hearing all these horror stories I think it’s time to try Zotero again before I begin writing the bulk of my PhD. Can anyone weigh in about its functionality with Word, using it between a Mac and PC and how it handles APA format? It’s been years since I used it.

  45. Endnote does have some glitches. A friend of mine warned me about Endnote and said if you are using it, always keep a fresh and upto date copy of your references in plain text as a stand alone word file. So you are backed up if things go wrong.

  46. Ok, got caught up in the hype over Mendeley, installed it, imported Endnote library, now face the task of single-clicking each and every reference (sevral hundred) to review details are correct (most of them are not). There is no batch process option. Finger poised on Remove/uninstall program….. Can anyone save Mendeley from an early death on my PC?

    • Can’t help you with Mendeley, but I think you would have a much better import experience with Zotero. We worked pretty hard to make sure that all the fields end up in the right places along with attachments. There are, of course, some fields that cannot be stored in Zotero at all, like Author Address, Publisher for Journal Articles (since it is never used in citations). Those would end up attached in notes, so it’s lossless (in a sense). http://www.zotero.org/support/kb/importing_records_from_endnote

    • Dean, that is why I am stuck at having 2 programs: I refuse to use Mendeley as my bibliography manager for PRECISELY the reason you mentioned above. I imported my 400 or so references into Mendeley and encountered the same single-clicking task as you.

      So, I use Mendeley for reading, note-taking, annotating, and “foldering” (organizing by folders). And NOTHING else. Peers of mine have told me they don’t have the single-clicking issue with Mendely that I have. I’m happy for them, but that problem has never remedied for me in Mendeley. So I use Citavi for my citation, bibliography, and knowledge management, and I’m elated. I copy and paste my notes and annotations from Mendeley to Citavi and from there use them to write, write, write and cite, cite, cite!

  47. I too was burned by the Endnote/Word combo- luckily it was before starting my PhD. All of course a week before a massive project report I’d been writing for 9 months was due. Out of habit from my undergrad days (when the fact that endnote even existed was AMAZING) I always work with unformatted citations. For me the solution to corrupted endnote references was to reopen the Word doc on my Mac at home, somehow, being a different program, Word for Mac kind of created a clean version which magically worked again.

    Like many institutions, my uni supports only Word and Endnote, but I decided that if things go so seriously pear-shaped in the middle of the night a few days before the thesis is due, then I’ll probably have to solve it myself anyway, in which case having a more stable option is much smarter. Although I now write mainly in Scrivener, a few years ago I got a MacBook Air which goes everywhere with me, and after much research settled the combo of Nisus Pro Writer as a word processor (native rtf format makes it easy to collaborate with supervisors etc on Word if needed and seems a bit future-proof) and Bookends as a citation manager- which I found to be one of the most clean and functional options at the time.

    I’ll hopefully be submitting at the end of the year, so its not the time to switch now, but with all this talk of Sente and Papers2 I feel some procrastination coming on!

  48. Wow deja vu! even down to the three computers (and I was considering a Macbook air) Running not walking to download and buy papers2.

    Thanks a million

  49. Following similar disaster with Endnote I moved to Refworks but never really liked it, especially after it updated its interface. I’ve looked at Mendeley and Zotero but finally settled on the ‘revolutionary’ idea of simply using Word. For something as important as my thesis I decided whilst the ‘bells and whistles’ could be useful, there were too many possibilities for meltdown. I now utilise Word’s Outline, Comments and Hyperlink features to add notes and divide my references into lists. Its very simple and via Dropbox, always accessible.

  50. I used Nota Bene. It’s not free and it doesn’t suit everyone, but I loved it. It includes word-processing software, bibliographical database, note-taking, reference collection and (crucially for me) the best non-Roman font system I know. Typing in Hebrew, including all accents and pointing, was a breeze. Trying to achieve this in Word or similar would have been hideous. But the referencing system was also excellent and made the final stages of the thesis, including generating the bibliography remarkably easy. There’s a free 30-day trial and I think it’s worth a look.

    • Oh, I meant to say that I was very impressed with NB’s customer support. I had a problem when I upgraded to Windows 7 and after several emails trying to find the bug, they phoned me and talked me through it at length and even suggested that if that didn’t work, they’d arrange in-person support while they were at a conference near my home.

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  52. Excellent post and exchange. For me it’s always about software making you compatible with it. Never a good thing. EndNote has always been fine. Clunky since day one and I _never_ use auto format. 🙂 Always keep the little suckers unformatted till the end and do the check to see that is all where it is supposed to be. I think of the software like a non house-trained pet. You just have to keep an eye on the damn thing the whole time.

  53. Great post. I totally understand how the suitability of reference managers really differs a lot across field. I initially tried Zotero and my favourite thing about it was how compatible it is with browsers, but recently switched to Endnote. The main reason I’m using Endnote is because most of the databases I use (legal ones) are configured very poorly for citation downloads with other reference managers apart from Endnote. Also those databases have almost no usable metadata which completely negates the Zotero function. I also like being able to view and work off pdfs in Endnote – working with pdfs in Zotero is very clunky.

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  55. Hi I used Endnote but because of lack of its ability to read metadata like Mendeley(2GB 😦 ) does gave way for exploring other reference managers. Although it is so far so good scenario but I hope you guys might have had this experience/ may comment on its reliability in the long run. I use a “papers of interest” folder for mendeley watched folder so that mendeley can pick pdfs on its own, and dropbox(>57GB) to backup the storage location of the mendeley software. I use a free Easy duplicate finder for finding duplicate publications for “papers of interest” folder. It is convenient for comment and note searches from within a single platform, (so far for over 2100 publications).

  56. Inger, trust me – Zotero all the way! First rule, anything computerish will crash so let’s never have too much expectations. Backups and alternatives are always handy especially for mammoth projects like the PhD research. That being said, I’ve had my computer crashed and lost my entire BSc Honours thesis. I have had my endnote for my master’s thesis crashed with gibberish (like yours) but was able to retrieve it from backup files. They say once bitten twice shy. Now, Zotero is my deepest love affair although I constantly migrant files between EndNote and Zotero (simply for backup purpose). Like any software, Zotero is constantly improving and I’m in on the journey to to defections. Anything free and innovative is a hook, especially for many students. EndNote is great but too expensive! So, thanks to Zotero’s team…I’m a loyalist:-)!

  57. I am still in love with Citavi, which I already used for my master thesis and now again for my PhD. Especially the publication assistant – one click at the end of the paper, and all my references are in the right style (even if I have no idea about that style, which happened a few papers back with a paper for a literature journal – completely different to our historical styles). Actually, citavi is the reason I till haven’t made the switch to Mac.

  58. I keep all my references in a text document which I write manually… old school, but no bugs, unless I do something stupid. Then as its in BibTex, it goes straight into my work with no problems. Well, after I got it to work the first time!

  59. I was subject to the same route through reference managers as you, except I did not try Zotero. I now use Papers2 for most of my needs, with a little of Menderley for the sharing of papers. The best combination in my mind!

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  61. Hi,

    I am doing my PhD using Scrivener and Bookends. The developer of Bookends even altered his program so that the APA format is correct both inside and outside parentheses using & or and. Both Scrivener and bookends are rock solid (have never crashed on me), cost very little money, and backup automatically (Scrivener saves every two seconds). I also save copies to dropbox, external time machine and the iMac. Scrivener for windows is less featured than its Mac sibling and bookends is Mac only. I used Note Bene on my windows PC but got frustrated with the time they have taken to develop the latest release. I am not a Mac fanatic but I have to say that the productivity increase from having stable programs more that justifies the cost of switching.

  62. thank you for this post, I’m still struggling to find the ‘right’ literature programme. For now I have settled for Citavi. It offers a knowledge tree which makes organisation of files really easy, one can enter tasks for each reference. Instead of ‘playlists’ one can create various projects. The only disadvantages are that is does not sync across devices and the note taking feature is a bit cumbersome, once notes are entered it is an amazing feature though.

  63. Thank you very much for this post. I came online in spite. I was disappointed with myself and my thesis. To cut a long story short, I came across a similar problem as your problem # 1. But the answer given by your supervisor not only made my day but my entire week. I want to dance and sing now
    I will also see Mendely and Zotero now that I have received one of the best news from this blog.
    Thank you Thesiswhisperer for existing.

  64. In case you have not yet found an alternative to Endnote, I would like to invite you to try our literature management software “Docear” http://www.docear.org. It’s free and open source with a strong focus on managing notes and PDFs. We store all information directly in the PDFs or in BibTeX and XML. So, you can share your data e.g. via Dropbox. However, if some advanced collaboration features (such as private groups) are a must-have, you are probably better off with Mendeley etc.

    And, if you have not yet found the perfect reference management tool, you might be interested in our Blog post about what makes a bad reference manager 🙂

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  66. Jorab! I regret to say this but Docear despite so many attempts did not work for me. After I made 2 projects, and 3 days, it just kept giving messages (alarms) of project not loaded.

    • I also was getting Docear errors “project not loaded”.

      I figured this out. My problem was I started editing the “welcome” memory map (filename tabs only show at the bottom IF you have more than one memorymap open – which I didn’t). And that “welcome” memory map wasn’t “in” any project.

      So the solution was:
      in left panel, expand the project, and expand “Library”.
      to open up the “Library” folder in the left panel
      right click on “Library” folder and click “Add Mind Map”
      Give it a name, and you get a blank memory map.
      Copy your work across, and go back to the old memory map. Menu -> Home -> Close current map.

      Now you have 1 working map in the project and no errors.

  67. Great post and love the blog – I’m about to start a PhD and this blog, including this article, has given me so many things to think about. Been looking at / researching / fiddling with different software for referencing, annotating PDFs on iPad, writing etc. I’m very keen to use scrivener but struggling to decide on a referencing system. I’m keen on Sente because it has an ipad app and is meant to be compatible with scrivener – but my question for anyone who knows is whether you can reference using footnotes in Scrivener and have it automatically generate shortcuts i.e. Ibid, shortened references for subsequent references etc (or at least have these generated from the references in scrivener when a document is compiled and put into word after the writing process is complete). Is this possible??

  68. I have been browsing this site during my MA, and am just about to start a PhD. I m a Scrivener convert. But have to plug my fave reference manager here – Qiqqa. It’s free for students, cheap for everyone else, and it’s flipping great to use. The team working on it are really engaged with their support forums – not perfect, but much better than many I could name and shame. It’s cloud based, keeps my notes, brainstorms and highlighting on pdfs, and lets me access them on android too!

  69. Stay away from Qiqqa – it will secretly watermark your entire pdf library besides it’s a fairly clunky/windows only app compared to some others on this blog. Great discussion otherwise.

  70. I have always loved Papers but wondered how people were finding Papers 3? I am beginning research Masters and was wondering about Endnote (less keen after reading this blog) or persevering with the changes to Papers3 to make it work for me

    • Papers 3 killed my dissertation.

      While many of the bugs have been fixed, it searches the internet all by itself, changes the data associated with each reference based on whatever webpage it finds based on a search of your article’s title. If you change the data back, it will ‘syc’ to its own erroneous version. If you give it a new webpage, say, for an Economist article, instead of gleaning data off that page it will find the only PDF associated with it (in this case, randomly, a statement on the Economist’s stance on slavery) and change all data (title, author, date) according to that PDF.

      I emailed support, and they told me the ONLY way to stop it from automatically doing all of this is to ‘unplug the internet’. I ended up having to correct over 500 citations. They refused to offer a refund even though it had only been a month.

  71. Used Bookends/Mellel for my PhD. Now using Sente. Just upgraded Papers 2 to Papers 3 because I was interested in its multimarkdown support. Unfortunately, still not reliable enough. Does funny things, throws lots of warnings and error messages. I’ll stick with Sente, nice interface and excellent iPad app.

  72. I used to use Zotero, which never worked perfectly on my Mac, but my PI insisted I switch to Endnote. Since he paid for it I decided to give it a shot. Well, about 30 minutes ago Endnote seems to have had a stroke and deleted almost all of the citations for an entire chapter of my PhD thesis. After opening a beer, and while crying, I started searching the internet for a solution. So far no luck, but at least I found an interesting blog, and I guess I will have to take my husband more seriously when he urges me to switch to Mendeley.

    • Depending on how long ago you tried Zotero, I would say give that another shot, it changes all the time. There are certainly no Mac issues we’re aware of. Perhaps there was an issue with your setup? Feel free to post to Zotero forums in the future if you run into issues.

  73. One vote for EndNote: I have been using it for almost 2 decades. First on a Mac, then on a PC, and now version X7 on a MacBook Pro, sharing a single huge library with 25K+ citations and PDFs between a BootCamp Windows partition and Mac OS X (the current license allows dual-platform use). I have not had any issues such as instability or loss of references. There are innumerable citation styles and connection options to libraries. Cite While You Write (CWYW) with MS Word has been reported to be problematic on the Mac side: so I would appreciate people’s text processing software recommendations other than MS Word on the Mac for working with EndNote. I have also looked at Mendeley. Without my existing EndNote investment, I would have probably started with LibreOffice and Mendeley. I did not fare well with Sente as I found PubMed use to be more specific an effective with EndNote. I imagine Sente to probably be probably best for people who also rely on iPads.
    What text processing software other than MS Word do people use on on Mac OS X for working with EndNote?

  74. Hi, does anyone have any recommendation for what works best with Scrivener? I was using Sente but it just isn’t working for me. I wanted to use Mendeley after many recommendations but it doesn’t work with Scrivener from what I can tell? Suspicious of Endnote. Any recommendations?

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  77. I use EndNote, I never tried anything else really. Last week I experienced a problem when trying to backup my references on my home pc. For some reason it would not stop indexing my pdf’s, luckily I resolved the issue (I am still not sure how). Other than that, Endnote is really helping me writing my review and wish I was introduced to it sooner. The fact that I can synchronize my references over the web and access them threw the internet or at home is very helpful.

  78. Like Endnote, Word’s cite-while-you-write feature is notorious for garbling your references and worse, especially if your references number 100 or more. To my knowledge, that has always been the case. A few years ago, I tried Sente and was very impressed with their support. That ended when I couldn’t remove the highlighting I added to a PDF and no one could figure out why. In addition, I found some references had to be manually entered even after the data was supposedly extracted from a PDF downloaded via the program. As I recall, the article was from the Journal of the American Medical Association (JAMA), so it was not a case of an obscure publication. When I asked the good folks at Sente if I needed to enter every author’s name (I recall there being at least 15) when the reference formatting style I had selected (AMA) would eliminate all but the first 3 for citations with more than 6 and ad “et al.” at the end, they didn’t understand what I was talking about. According to their manual at the time, there would be no need. Repeated explanations on my part failed to elicit a solution and there was response from the forum. About a year later, I tried Zotero. I didn’t like the crude interface or the slow response when I needed help. Another problem, and major one for people in the sciences, is that Zotero’s output of references in a document failed to include italics for binomials, such as plant names. There were a number of discussions about this and it seemed that everyone but the people at Zotero understood their importance. Imagine having to go through 100s of citations just to find and italicize names. Mendeley sounds tempting, but somewhere, perhaps in an earlier post, I read that it has the same problem of removing highlighting from PDFs. The overarching problem is is that none of these programs are ready for prime time. Each one is an experiment and the users are the proverbial guinea pigs. They tout this and they tout that, but the developers don’t seem to realize the costs of downtime when what they promise fails to deliver. I blasted the folks at Endnote over the phone and delivered a verbal lecture to Microsoft for similar failings. The folks at MS giggled and the tech person at Endnote told me the program was never meant for a personal computer, or was it the other way around? The bottom line is that either corporation is causing untold grief and millions in downtime. Can anyone assure me of a citation-come reference mgtm program with cross-platform compatibility that does not have serious issues?

    • I can only speak for Zotero and, while perhaps Zotero’s interface is not that shinny, I am very surprised to hear that you received slow responses on the forums. It’s possible that a thread was overlooked at one point or another, but we typically try to respond within an hour (unless it’s a really awkward time… most of us are U.S.-based) and 99 times out of 100 we will respond in one way or another within 24 hours. Perhaps you find real-time support necessary for your needs, which, unfortunately, Zotero cannot provide.

      Additionally, italicizing (as well as superscripting, subscripting, bolding, small-capping, etc.) parts of titles has been possible for quite some time now (at least 2 years), so maybe you tried Zotero a long long time ago and I would certainly suggest checking it out again. A LOT has changed since those days.

      • Thanks for your reply and thanks also to the Thesis Whisperer who deserves a big hug. I confess that it has been about 2 years since I last tried Zotero. Hopefully, things have improved. When I referred to italicized words, I meant that even when references within Zotero were already correctly italicized for binomials in article titles, the output in one’s citations were not. Journal titles were italicized, however, so it was a mystery to a number of science-based writers who also complained of the problem as to why Zotero would neglect to address such an important need. A response within hours would be incredible, even for someone living in North America, as I do. Sente was the best for quick responses, but that was only in my experience and from a couple of years ago.

      • Yes, that’s what I meant by italics support. It seems to be able to do what you want. I’d encourage to give it another shot if you’re looking for a reference manager.

  79. I second the recommendation for Zotero. I’ve tried several other apps but Zotero is the best all-around ref manager in my opinion… and it’s free and open source! The latest Bookends (Mac only) is also worth a try. I believe there is a fully functional demo version for up to 100 references. On the Window’s side I recommend Citavi (and hopefully in a Mac version soon), also with fully functional demo.

  80. Pingback: Book review: Mendeley | The Thesis Whisperer

    • It’s a great choice it you have a little more time to get into it and it will save you a lot of time down the road when you come to write up. downsides: only Windows at the moment.

      It’s a freemium product and the free version has the core functionality with adverts. Also you can have all your papers locally, or if you want to cloud sync, you can get 8 Gb storage with premium or you can pay a couple of dollars to cover the cost of the storage: http://www.qiqqa.com/About/UnlimitedStorage

  81. Pingback: Ahh Mendeley and freemium tools | The Weblog of (a) David Jones

  82. You really make it seem so easy with your presentation but
    I find this matter to be really something that I think I would never
    understand. It seems too complicated and very broad for me.
    I’m looking forward for your next post, I’ll try to get the hang of it!

  83. Linking to your website is not recommended at all.

    3 Check-out web design processThe check-out process starts with the results properly.
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  84. Pingback: Citations, citations, citations…. | Prof. J's Blog

  85. One of my friend was just crazy about Papers. I saw her used it on her Mac and I was completly convinced. However, when I tried to use it on my PC, the whole affair turned into a complete and utter disaster. I had switched just before a tight deadline and therefore had no time to look at the whole document to check if everything was ok. It turned up it wasn’t. The whole document was a complete mess. My director was disapointed and I will never use that program again. They shouldn’t have released it on WIndows if the compatibility wasn’t alright.

  86. REALLY really useful discussion, folks! Thank you.
    This is what human history needs: Learning from the mistakes of others gone before.

  87. I agree that finding a reference manager seems to be a personal thing! I used Papers2 for ~1.5 years. For more than 8 months it happily synced between my work PC and my home Mac laptop. Then one day, no rhyme or reason, two thirds of my library disappeared, and some papers got magically renamed as different papers. Papers2 staff were less than sympathetic, or helpful, and simply told me that they can’t guarantee success for syncing between Macs and PCs.

    I jumped shipping to Mendeley, and while its not perfect, its been really good to me and haven’t had any problems syncing between computers, which is the most important part to me! Mendeley support has been even better to deal with than Papers2, and its all for the fine price of free.

    2.5 years later I’m still periodically discovering missing references in my library from the great Papers2 crash – the hate you feel for Endnote, I feel for Papers2.

  88. There is a new kid in the block.
    Just tried it and it is amazing,
    I compared their PDF parser with the one from Mendeley and it is just much better and even much less buggy…
    They say it is closed beta but you can try to ask for access…


  89. Pingback: Thesis 2.0 Bonus | Secret Internet Marketing Blog

  90. Pingback: How Mendeley Helps PhD Students Become Successful Scientists | The Thesis Whisperer

  91. would Zotero or Mendeley work with an unregistered version of MS word 2010? I am unable to continue using Endnote because I am no longer eligible for the licence I had for MS Word. I am therefore looking at open source software but unsure if having an unlicensed version of word will still be a problem

  92. Pingback: Referencing rage – EndNote vs. Mendeley (and RefWorks) | NeuroRach

  93. Just a follow-up as someone who is a paid EndNote and Sente customer: Sente is practically unsupported. It does not import PDFs without error. The developers are not responsive at all. The application has not been updated for a long time. It seems they have abandoned the project and just trying to sell whatever they can. EndNote on the other hand is constantly updated and has an active support system including excellent forums. EndNote does more than Sente while Sente does some things better (PDF annotation, browsing, and a more OS X compliant GUI).

  94. Thank goodness for pages like this. I used Endnote for my Honours and Masters and I swear I’m never going back. It’s fine for short pieces but when you use it a lot it starts doing weird things like putting random commas and full stops everywhere so that you have to ask for professional assistance in a forum because you just cannot figure out what’s going on. I’ve just started a PhD and hopefully I can find a less hopeless reference manager!

  95. Hi all. I am writing a research Project for my Fellowship at Sydney, use Mac and am new-ish to EndNote. Importing unformatted bibliography from Word to EndNote was a huge problem but got over that with EndNote Support who suggested to use wizfolio.com, a 3rd party software (ridiculous that they don’t have something decent themselves), took a long roundabout while. Can’t use Safari to import from databases, have to use Firefox, ok, downloaded their latest version. But do you think that Firefox would have a plug-in for EndNote X7?! No, neither for the previous version, tried that, too. So, no plug-in, hence no toolbar, hence no “Capture” possible for webpage references into EndNote. Precious time kind of wasted (2 weeks or so) on all this banging the head against the thick EN wall. Maybe time to give up on it, and look elsewhere. A bit rushed for time re the deadline to submit the Project, not sure of the next step; from the above forum, Mendeley, Zotero, Citavi (if Mac-ready)? All have followers obviously. Help! I have 150-200 references to use, easy import (too much to ask?!) and auto PDF import would be good, even if not all, from free sites as i am not embedded with any university database. Huge kudos to the thesis whisperer (GSOH) to have started this ball rolling! Thanks heaps.

  96. Pingback: Managing the Sluff | The Thesis Whisperer

  97. My university promotes EndNote, so I tried that for a while, but said goodbye after my references got messed up. Recently I started using Widiem (http://www.widiem.com), a cloud-based solution. I didn’t have too many references to import from EndNote (100-200?), but it went smoothly. What I like is the great UI, and the fact that I don’t have to do A-N-Y formatting. The downside is that there is no PDF storage/management.

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  99. Pingback: Reference manager 101

  100. Pingback: Choosing a Citation Manager: Mendely vs EndNote vs The Rest? | Factors I Consider

  101. Pingback: Reference Managers | Urban Speeches

  102. HI,

    Does anyone know of a program that will ‘read’ my bibliography and match the list to my in text references? I omitted to use endnote and the like in my dissertation and the journals I want to publish in have a different referencing style. So now I am left with the consequence of my decision not to use end note and will need to manually change the reference styles for my papers to match the journal. Is there another way?

  103. I use a combination of Excel and WorkFlowy. Let me preface this by saying I previously used zotero & tried others like endnote, mendeley,…. I never liked any of them. I used zotero the most, but only because I felt I had to use something. This is until recently.

    Now I use excel and workflowy solely – it’s amazing. Soon I will post an entire write up of this workflow process on my blog – that might take a few weeks though.

    Excel, I only use to keep a backup of my important citations. Workflowy does the rest. Listen, workflowy is just a “simple” outliner. It has simple features and this makes it amazing. This makes you the designer, the creator. Workflowy has also forced me to be a citation guru. I mean, seriously, I found myself at Purdue OWL every time I made a citation. Plus I relied heavily on zotero to auto-format my citations. Not anymore. I pull the info I need for my cite and put it in my outliner and move on. When I need to create a bibliography I use the old-fashioned copy paste method. It works beautifully.

    I’m excited to demonstrate this for anyone who is interested. I think you will like it too. You can find my link in the “read some PhD student blogs” section, near the bottom, I believe. Again, I will post this write-up, hopefully, before the end of March 🙂

  104. If you’re just starting a Ph.D. I would seriously recommend learning how to use Latex / JabRef. Both are free and once you get over the learning curve they are *incredibly* powerful and easy to use and difficult to break 🙂 . The website overleaf.com provides a ready to roll template for beginners, in addition to a version management / collaboration system. I wish it existed when I did my doctorate!

    Latex made it easy for me to re-format submissions to journals, it was usually a single cut-and-paste from one template to another and a re-compile. I never worried about references not working, all i had to do was type ” \bibliography{my_thesis} ” and it would take care of itself. Likewise, tables, figures, tables of contents etc are easily taken care of. The Word “jumpy figure” was enough to put me off putting pictures in Word documents, and my thesis had well over one hundred figures.

    I still use Word grudgingly for short docs, would never use it for anything large or that needed tables, figures or references. I used Latex for my CV and have been told (more than once) that it helped me get interviews. Really! There are plenty of incredible templates out there.

    I wouldn’t recommend Latex for everyone. For example beginners who need something finished quickly will struggle (although overleaf has a compiled template you can copy/paste to easily enough). If the journal you plan on submitting to insists on word templates then you’ll have a bit of copy/paste to do (unheard of in sci/eng, can’t comment on the humanities). Learning a markup language can be daunting at first but in the end I saved myself a ton of headaches when it came to writing up. I also went on to learn HTML (the next logical step) and now have a little sideline in developing websites for friends! You can’t beat learning something new, or the satisfaction of creating a beautiful document.

    Some nice examples:

    • I made a somewhat similar comment when this post was new and has since then been puzzled over the many commenters (I am tempted to use another word…) who insist on using inferior and error prone tools with low flexibility and, often, a hefty price tag.

      There are good and free-of-charge solutions out there, sometimes since decades, and nobody knows about them…

      Then there is an endless list of bull-shit tools, and THESE, for some incomprehensible reason, are not just well-know, but raised to the skies because they allegedly, “finally” solve a problem that in reality had been solved while the commenters were still in kindergarten.

      In many ways, they remind me of someone using a child’s plastic hammer to drive nails into a wall. If someone wants do to work on a professional level and in professional quanties, he needs to pick up professional level tools. Not plastic hammers, not MS Word, and not the latest “hip” way to do references.

      Truly depressing!

    • Amen, I couldn’t agree more with everything said here!

      I also used LaTeX for all kinds of documents (including CV) during my studies and Ph.D. and Word for short documents, cover letters etc. It was uphill for the first couple of student reports written in LaTeX, but I am extremely grateful for having learned to typeset reports, theses, papers and much more professionally with LaTeX.

      Also, for references, JabRef is an excellent choice. It is free, but feature-rich, which makes a lot things and customization possible. Initially, I just used it for managing references for my M.Sc. thesis, but during my Ph.D. I turned it into my literature database. I also considered the more modern options – like Mendeley – but in the end was very happy with what JabRef did for my ~500 references.

  105. Pingback: EndNote … I quit! | En Kolding

  106. Pingback: Choosing a Citation Manager: Mendely vs EndNote vs The Rest? – Michael Wilson

  107. Use Qiqqa – it is vastly superior to Zotero and Mendeley because it’s bibtex sniffer quickly allows you to choose bibtex with the correct coding. (In any case Mendeley several times missed an author – which means that I would never ever use Mendeley with that risk !).

  108. Just thought I’d add my issues with mendeley as a search of how to solve them brought be here.
    Firstly, in citations it is including http://doi.org/ rather than just doi: and then the number. The only way I can figure out how to solve this is to cut and paste the reference list on to another word doc, use the find feature and remove them. Really annoying.
    Also, it won’t correctly cite theses. Missing the city and country they were written. As well as if it was published or unpublished.
    Lastly, I think, it keeps randomly adding the author back into the body of the work when I have ticked ‘suppress author’. No reason why, no order to it. Just have supervisors constantly showing me where it is happening.
    I don’t feel any better having said all that. damn it.

  109. Pingback: How to get into a PhD program | The Thesis Whisperer

  110. I used EndNote about 4 years ago and switched to Papers due to a recurring software bug that just never was fixed. This year I tried going back because I like the ‘idea’ of Endnotes and how it supposedly integrates into multiple academic reference systems. This time, I paid for the upgrade, only to have it freak out because I had previously registered. After numerous emails and a several weeks of going back and forth through tech support – they can’t fix it. They want me to go online between 1:30 am and 7:30 am (Eastern time) for a live tech trouble shooting session. My final analysis – it’s buggy, Thompson doesn’t appear to be willing to invest in adequate customer support, and frankly, its a bit of a train wreck. It works beautifully when it works, but frankly, for paid software, the degree of reliability is incredibly low. I wouldn’t encourage anyone to buy it.

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