Why am I still using EndNote?

15 July 2010 by Andrew Sun, posted in Uncategorized

Why backing up data online?

I deem syncing everything online practically beneficial and crucial to my research. Of course not everyone around me put their important data online. They remember to backup their work routinely and in multiple places offline. I once heard of a PhD candidate who backed up his unfinished thesis on as many as 4 places: two computers and two USB flashes, but 3 of them crashed simultaneously in one day. So the wisdom of backing up things is never being too optimistic on your luck. Considering the worst luck may be the crash of the WWW, straightly put your work online and auto-synced is the safest backup strategy. Fortunately this means not more but less trouble than only syncing your work among numerous offline places which still have higher possibility to crash simultaneously than the crash of the whole Internet.
However, practically the safety of putting things online is reduced to that of putting things on one or two online services, which means only the crash of these services is sufficiently unlucky. So choosing a big powerful service provider is very important.
Things that will become handy when they are auto-synced includes 1) files in my work folders, 2) my big, all-in-one note, and 3) my reference library.
The 1st aim is exclusively met by Dropbox, which I still manage to use even though it’s been censored (blocked) by China. The 2nd aim was previously met by MS OneNote. I sync the my note there by putting its local folder in My Dropbox. However I always hate MS Office of versions later than XP and OneNote only appears in Office version later than 2003. So installing OneNote means I have to install two versions of Office in one machine (XP and 2003) which is far from comfortable. Recently I tried Evernote and soon paid for a premium account. The 3rd aims, reference manager, is still met by EndNote.
Dropbox seem rigorous in stability and bright in its future fate, so does Evernote. I don’t need to worry about its future bankrupt. Anything of Google is also safe from bankrupt too. These are services that are very unlikely to be terminated. People say that cloud storages never crash. The Dropbox and Evernote are also growing and expanding into the only best choices, monopoly among their counterparts, like what Twitter and Facebook now are. Saving data in these services is similarly safe to saving them in the entire Internet.

Why do I tried Mendeley so late?

Martin has talked a lots about the web 2.0 reference managers. I tried some of them, too. Although I have been using a reference manager long enough and will never again meet the tough task of manually adding a lot papers into a database, there are still many people around me who tried a reference manager very recently. Importing records from PDF files is the biggest problem that prevents first-time users of reference managers, and according to Martin’s RM Overview only the Mac-based Papers and Mendeley support this function. As a Windows user if I am asked to recommend a reference manager that people will more likely to try, Mendeley can be my choice over EndNote.
But for my own purpose, having been tried many online reference managers myself, now I am still using EndNote. I had to stop using Zotero when Google Chrome became my default web browser, and Mendeley used to crashe a lots at that time. CiteULike and Connotea don’t support Cite-While-You-Write feature. I heard that it fixed most bugs that cause crashing. But it still have much space to improve.
First, entries that were imported directly by PDF files cannot be too many, or Mendeley crashes. I knew this when trying to watch a folder with 1,147 PDF files by Mendeley. After it imported all the files, the whole program became too slow and responding too discontinuously to be usable.
Second, the customizability is too low. There are many functions I want to work slightly differently. For example sometimes I don’t need it to auto-delete the duplicated entries during importing. And I would also like to configure fields to display in the citation list, which is now fixed as “Authors, Title, Year, Published In” and not customizable. You can’t sort the list by more than one field by ascending or descending order, either. The worst thing for me is: it only support Word 2003 and as I mentioned earlier I hate Office 2003 and later versions.

Why only EndNote is the best?

Designing the best reference manager is very easy: Just be an online and PDF-recognizable version of EndNote!
Why does Zotero only release a Firefox plugin? Why does Papers only support Apple products? And why doesn’t Mendeley tune its database system better and faster? Why not just copy all EndNote’s functions and customizibility? - I mean EndNote cannot reserved any copyrights of “having these functions” so why cannot other developers see the already successful EndNote? At least as a database a reference manager should support advanced searching and sorting which Mendeley lacks. And specifically a reference manager should allow users to create new citation styles but Mendeley does not. By the way I don’t need to view the PDF in a reference manager because Acrobat Reader is always the best PDF viewer and free for download. One feature that’s enough to make Acrobat the best is: it allows split view, or can someone tell me another PDF viewer that can split the viewing window into 2 halves, so that I don’t need to scroll back and forward between a paper’s main texts and reference lists, figures, tables, etc.? Mendeley does not support split view, at least, and including the PDF viewing function makes the program very unstable and slow.
I’m not blaming Mendeley alone, but using Mendeley as an example to ask why there is no one product that can fill all blocks in Martin’s Overview diagram with its color — given that the entries in the diagram is not hard to thick of before Martin drew the Overview? Having all features can sometimes make a software huge, like MS Office, but this is not the case for reference managers if they are simply online and PDF-recoginzing version of EndNotes.

14 Responses to “Why am I still using EndNote?”

  1. William Gunn | Permalink

    Thanks for your comments, Andrew, and I appreciate you recommending Mendeley.

    You’re correct that Mendeley has struggled in the past with large batch imports. We’ve made some changes in the recent release to address exactly that, so I would suggest updating to the most recent version and then letting us know if you still experience slowness on imports or in the PDF reader. They should both be quite fast now. We’re also aggressively adding capacity and trying to keep up with demand, so please bear with us on that.

    With regards to your specific feature requests, you might want to enter them at http://feedback.mendeley.com As you can imagine, it’s a difficult struggle to balance ease of use with an lengthy feature list.

  2. Andrew Sun | Permalink

    Hi, William.

    My comments are very personal and may not reflect the most common view. I am using the latest Mendeley and frankly speaking it does not crash too frequently.

    As I’ve mentioned I personally don’t care much about the PDF viewing feature so having the PDF attached to the entry is not important for me. I imported the entries without PDF watching instead and Mendeley became perfectly smooth.

    I’m also learning the CSL syntax.

    I guess what Mendeley wants to be is too new and there is little or no existing algorithm or resolution proven to be stable and powerful to adapt from. Mendeley fills the most blogs in that Overview diagram so it’s still the best, though not enough.

  3. Mike Fowler | Permalink

    Andrew, one simple answer to your main question, is that the two leading alternatives to Endnote (in terms of user features, at least), Mendeley and Zotero, are (essentially) freeware, although you can give Mendeley money for online storage facilities I think.

    Endnote can afford to employ a large enough team to design and constantly improve their software, but that comes at the cost of a licence fee, although this is often covered by your hosting institution. Personally, I don’t think public money needs to be spent in this way when suitable freeware alternatives exist. The question is: are the freeware alternatives suitable?

    Incidentally, Zotero citation styles (CSL) can be modified relatively easily (e.g., see here). Never tried with Mendeley though. Zotero also work very nicely with OpenOffice, which should help you avoid using overblown MS office products. It’s almost worth having Firefox just to run Zotero!

  4. Susan Steinhardt | Permalink

    Andrew, what a great look into the leading online reference managers as well as an interesting idea for designing ‘the best’ one. What do you think of a laboratory or project management tool that incorporates reference management?
    Have you seen BioKM (http://www.biodata.com) which does exactly that (specifically with EndNote). Definitely would makes it easier to see the big picture of your research!

  5. Nicolas Fanget | Permalink

    I think Martin has updated this table somewhere, Zotero can extract metadata from PDFs nowadays. It can sync all your files to a WebDAV storage too, which means you can purchase storage from someone else than Zotero or set it up yourself if you want to do so.

    Although I like the idea of Mendeley, it has never worked for me, either crashing or not importing things when importing my library. Not sure why.

    I have also vowed to use either open source software or/and open standards whenever possible, because of a bad experience with EndNote (would have happened with any other proprietary system).

  6. Mike Fowler | Permalink

    Nicolas (et al.), I posted about Zotero and non-prop software last year and have been happily using Zotero since, even managing to introduce it to my new group.

    I submitted my first MS written only with Open Office and Zotero in March this year. The only headache was figuring out the equation editor in OO, all else went smoothly. I even managed to modify an existing citation style in Zotero to match the journal’s required style with little trouble.

    Here’s a handy Zotero Reference Test Pane to help with that.

  7. Nicolas Fanget | Permalink

    Hi Mike, I have read that post from last year and I can only agree with you that Zotero is right now the best alternative I could find to EndNote (YMMV).

    I really appreciate the fact that I can sync my library between my work and home computer(s) easily, and access it online too. It looks like great things are in the offing for that software. I would second your comment about installing FireFox just for Zotero as well. At home I usually browse with Chrome but have FF at hand for all reference-collecting/citing purposes!

    The link you give for the CSL editor does not work for me, but you can copy this: chrome://zotero/content/tools/csledit.xul and paste it in a new tab. Done!

  8. Andrew Sun | Permalink

    @Nicolas Good to see that people love Zotero so much that they install FireFox just for it. I think they like it with reasons about usability besides their tendency to use opensource/open-standard softwares. You and other’s comments here strongly prove the success of Zotero. However, I still think that the FF-just-for-Z idea is not comfortable and convenient.

    @Mike I know the economic reason but I did not mention in my text which was indeed unfair. However, no doubt I will paid for “the best one” if it exists, so what I wonder is the possibility without the constraint of money.

  9. Jen Melinn | Permalink

    Hi Andrew, interesting post and discussion. To build on this, and particularly your statement “Designing the best reference manager is very easy: Just be an online and PDF-recognizable version of EndNote!” you should know that the latest release of EndNote does include the ability to read metadata from pdfs and create records from them. There’s also Cite While You Write for OpenOffice on Windows. And I don’t want to plug too much, but take a look at EndNote Web.

  10. Frank Norman | Permalink

    You have made it clear why it is so hard to answer the question “which referrence manager should I use?”. The tool you use has to fit into your workflow, your personal combination of other tools used, your environment, your personal preferences. Not to mention the problems of finding time to switch to a new product.

    It is always tempting to think that it would be easier if we all used the same product, but it isn’t going to happen!

  11. Nicolas Fanget | Permalink

    Indeed Frank, the answer to that question is down to the person just as much as it is down to the product!

    This is why I am favouring computing standards, I don’t want to know whether you’re using Windows, Mac or AIX, I just want to be able to share data/collaborate with people!

    I would dearly love to be able to use a reference manager that can identify what the refs are in a manuscript, and edit/import them, no matter which program was used to insert them. I understand this would be possible only if reference manager developers agreed on a standard. Since we don’t even have a standard for rich text writing (well, there is RTF but not full-featured, and after that you have the ODT vs OOXML war), that’s a long way off, unless someone can pull off the web collaboration thing.

  12. Sebastian Karcher | Permalink

    I’m late to the debate, but this is an odd post.
    For some reason you seem to assume that Martin’s list of features is exhaustive and then you leave out the ones that you don’t care about to end up with:
    “Just be an online and PDF-recognizable version of EndNote!”
    just some thoughts of things other people might care about that EndNote doesn’t have:

    - collections and with that hierarchical organization structures
    - the ability to switch from a footnoted style to an author-date style in one click
    - a more powerful citation language that allows for conditional testing of variables, groups etc. – .ens styles are not very powerful.
    - works on Linux
    - loss-less export formats. Endnotes RIS format is old and has many problems. Formats such as RDF or Zotero’s open standard (which allows Mendeley to Sync with it) have a much lower degree of lock-in.
    - better ability to work with web-pages and other online resources (NYT, BBC, Guardian etc.)
    - better integration with LaTeX and LyX

    - and until the very recent release of X4: full-text search in pdfs, add items by ISBN, DOI, or PubMED ID, cite-while-you-write in Open Office

    Those are just some of the things Endnote can’t do that I care about (Zotero can do all of these, Mendeley most or all of them).
    Others, I’m sure, will have plenty more.

    So no, Endnote is absolutely not the standard anymore. The idea that either Mendeley or Zotero are “simply online and PDF-recoginzing version of EndNotes.” just shows that you’re not very familiar with them.
    Endnote is losing ground and trying desperately to catch up to Mendeley’s and Zotero’s innovative new features.
    Some people – for one or the other reason – still prefer Endnote and that’s fine. But to claim that Endnote should serve as a model for it’s competitors, who have been able to challenge it’s status within the 3 (Zotero) or 2 (Mendeley) years they have been around is a truly strange claim.

    Add to that the fact that Endnote would have far fewer users if University libraries wouldn’t spend thousands of dollars every year subsidising it…

  13. Andrew Sun | Permalink

    @Sebastian The title of this post is Why am I still using EndNote. And you also shared why you are not.

  14. James Herrick | Permalink


    I use EndNote and recently switched from Firefox to Chrome. Now EndNote doesn’t automatically open a citation when I download an EndNote-formatted citation. Did you have trouble with this? Can you tell me now you formatted Chrome to do this? I can’t find any preferences/applications area to edit in order to specify applications to open specific file types (as one can with Firefox, etc.).

    I know this is somewhat off topic but I noted above that you said you used EndNote and Chrome and figured you must have found a way to do this. The problem came up today in downloading from American Society for Microbiology journal sites (AEM, J. Bact, etc.). Thanks.



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