Several General questions for the audience...

EightmanVT
Hi all. I am rekindling some long dormant research and am finding that I need quite a bit of brush up on my tools. One of the things I've been 'researching' are the different reference management software tools out there. I think I've narrowed my choice down to either Zotero or Mendeley - but after trying Mendeley, albeit for a very short period, I'm not sure it's the full solution I'm looking for. My needs are pretty simple - and I doubt unique. In fact - one of the links I stumbled across had a lively discussion with some of the key stakeholders chiming it - and the OP and a few other posters had similar requirements as mine. Unfortunately - that thread never really reached a conclusion, but it's also 6 months dated now.

http://chronicle.com/forums/index.php/topic,71426.30.html

My field is Electrical Engineering. I'm looking for a reference manager that will allow at a minimum


* Ability to manage pdfs, other document types as well would be preferable
* Automatically extract citations, keep running citation list,
* Customizable citation formats
* Automatically sync references to the 'cloud' and across platforms including the iPad.
* Use with Windows and Mac OS X (related to the above)
* Allow multiple notes in a particular reference and enable exporting of those notes, exporting associated citation with the notes
* search papers and notes
* interface with Word 2011 (Mac)
* Attractive and usable UI
* grab references from the web quickly and easily
* accurately pull citation information from articles and papers
* Easy to learn
Those are some of the primary things I'm looking for. I originally decided against Zotero and in favor of Mendeley primarily because its requires Firefox - and I just refuse to put Firefox on my new machine. It's just a slow, leaky browser compared to others out there (Safari, Chrome). However, Mendeley doesn't have a real user forum, at least that I can find. They haven't responded yet to questions posed - and it appears that many of their user suggestions remain without feedback. Makes me wonder if they've slowed down support of their primary SW – perhaps distracted by fixing bugs with their iPad app. I'm starting to wonder if Zoltero is a potential solution – as I've read that it may handle notes in the manner I've described – whereas – I can't figure out if Mendeley does. At any rate – I'm seeking an opinion here. Yes – I realize I may be reaching out to a biased audience – but I'm not quite sure where to solicit an opinion outside of some place where researchers are likely to congregate with similar needs – like this forum, I would assume. I see that Zoltero is developing a stand-alone version and I was wondering if it fits the description above – and more. Is it stable? Can I forego Firefox and stick with Chrome? Etc…
Thanks
  • bdarcus
    Given that both applications are free, why don't you just put them through the paces and determine for yourself which you prefer?
  • EightmanVT
    Well - that is certainly one course of action which I've considered - and potentially will end up executing. I guess I'm trying to accelerate the "research of the research process" - rather than building 2 separate libraries, etc etc. I'm itching to get to the business of completing this research project to which I've assigned myself a very aggressive completion date. I've spent the better part of this past weekend reading extensively, and almost exclusively on this topic. I had quite a few hours invested before initially deciding on Mendeley for some of the reasons I already listed. However, I'm now concerned it's lacking some key features - and before I put all of my focus on literature and the actual research at hand - I want to get my workflow defined. I also don't want to install Zoltero if it's not a mature package yet. I was interested in feedback regarding my wish list before deciding to add another application to my new MBP.
  • noksagt
    I think Zotero can do all of what you listed (but many are qualitative metrics). Bruce is right: try it on your own, as this is subjective (for examples, others share your opinion that Firefox can be slow, but disagree that it wastes a lot of memory).

    Zotero on Firefox is considered stable. The stand-alone version and extensions for other browsers are in alpha release at this time.

    Firefox+Zotero are easy enough to install if you don't like them & Mendeley will sync with Zotero.
  • adamsmith
    Let's go one by one:
    Most of these have threads about them, so if you're interested in a particular issue, spend some time searching, it'd probably be a bad idea to rehash long conversations here.

    * Ability to manage pdfs, other document types as well would be preferable
    Zotero can do this, but it won't put your files in a folder structure of your choice. You can use virtual folders to get all pdfs in one folder, but otherwise the best way to access files is from within Zotero.

    * Automatically extract citations, keep running citation list,
    I don't quite understand ("running citation list" leads to this blog post as 1st google hit...), but if you mean extracting reference data from a regular formatted bibliography and keeping a list of which reference you cite in document the answer is basically no.

    * Customizable citation formats
    kind of - csl is customizable and not very hard to learn but no GUI - a GUI style editor is in the works from Mendeley (which uses the same format), but the fact that is has been long overdue doesn't make me optimistic.

    * Automatically sync references to the 'cloud' and across platforms including the iPad.
    sync yes, iPad no, some people do it but it's clumsy and takes some extra effort. Hope is that Z Everywhere will make this easier, but I doubt there'll be an i-app for Zotero anytime soon.

    * Use with Windows and Mac OS X (related to the above)
    yes.

    * Allow multiple notes in a particular reference and enable exporting of those notes, exporting associated citation with the notes
    yes and no - yes multiple notes attached to a reference and export, no to making note _in_ an article (e.g. a pdf) and exporting them.

    * search papers and notes
    yes.
    * interface with Word 2011 (Mac)
    yes.
    * Attractive and usable UI
    I think so, but that's a matter of taste.
    * grab references from the web quickly and easily
    very much.
    * accurately pull citation information from articles and papers
    yes.
    * Easy to learn
    yes.
  • ajlyon
    Zotero on Firefox is considered stable. The stand-alone version and extensions for other browsers are in alpha release at this time.
    There is also the very nice compromise of running the Zotero+Firefox beta (more polished than the standalone alphas) and having the Chrome/Safari extensions send their citations there. That's what I'm doing, and it's a pleasure. It's a little bit heavier than Zotero+XULRunner (= Zotero Standalone), but you lose none of the functionality of classic Zotero. Just enable extensions.zotero.connector.enabled in Firefox's about:config.
  • EightmanVT
    Hi - all. I really appreciate you taking the time to respond. I think the notes feature might be the discriminator for me - as I don't see the ability to do this in Mendeley. Yes - you can have multiple notes, but I don't believe they can be formatted (If so - it's relatively limited but I'll have to check this evening as I'm not on that computer right now), neither have I figured out how to export these notes anywhere - although I have a question in to Mendeley support.

    The ability to take notes as I review literature -and then search them - based on a set of tags or keywords - then export and maintain the source or citation info is to me key. Should assist with streamlining the research process significantly.

    I may have to just bite the bullet and use Firefox for a while.

    @ajlyon - I'm not certain I understand your suggestion. Are you suggesting running both Firefox and Chrome simultaneously - but using a Chrome plug-in to export citations to Firefox?
    Thanks again.
  • adamsmith
    @ajlyon - I'm not certain I understand your suggestion. Are you suggesting running both Firefox and Chrome simultaneously - but using a Chrome plug-in to export citations to Firefox?
    yes.
  • ajlyon
    edited February 9, 2011
    Yes, that's what I'm suggesting. If you prefer Chrome for your normal web browsing, you can keep using it, and install the Zotero extension. It has to send its citations somewhere -- usually to the standalone Zotero. The standalone isn't that polished yet, and it is missing some functionality right now, so I suggest running the usual Zotero extension in Firefox and setting that configuration option, which will allow you to save citations from Chrome to your Zotero library. That will also let you use Firefox to access certain websites from which the Zotero extension for Chrome still has trouble scraping bibliographic data.

    If you do run Zotero in Firefox, you might as well enable this preference and install the Chrome extension, because it will give you citation-saving capabilities from either browser.

    This all made a lot more sense in the graphic that Dan Cohen had in his Zotero Everywhere presentation, but I don't know where to find it.
  • RintzeRintze
    This all made a lot more sense in the graphic that Dan Cohen had in his Zotero Everywhere presentation, but I don't know where to find it.
    http://hatorikibble.wordpress.com/2010/09/22/zotero-everywhere-sogar-im-internet-explorer/
  • ajlyon
    Hmm. I thought that the slide had the plugins feeding into standard Zotero as well. Well, add a line from them to the Firefox icon, and that's what you should keep in mind.
  • EightmanVT
    @ Rintze - I think I follow the graphic - hopefully the rest of that page isn't critical to the understanding as my German is a bit rusty - meaning - I know approximately 2 phrases. :-) But thanks for the link.

    @ Adam - Thanks. One thing is certain - it's already easier to get answers about Zotero than I'm finding it with Mendeley.

    @ajlyon - Thanks again. I guess I'll pollute my nice new MacBook Pro (new to Mac as well) with the new Firefox beta this weekend - and give Zotero a run through.
  • John_muccigrosso
    Could the info on the about:config connector pref get added to the hidden prefs page? And maybe also to the short page on the standalone? There's a reference to using connectors there, but not to the about:config part in FireFox.
  • adamsmith
    we'll have to think how to deal with the beta version in documentation - I wouldn't want to include things that don't exist in 2.0.9 on general documentation pages at this time. On the other hand it'd be annoying to double the entire documentation.
    We'd probably need a better summary documentation page for 2.1b as the best solution.
  • John_muccigrosso
    I think it would be good to have the standalone page fully explain the situation with the hidden pref, even if it doesn't go on the hidden-pref page yet. It's here in this thread after all and a search like the one I used to get here would easily find it.
  • EightmanVT
    I don't quite understand ("running citation list" leads to this blog post as 1st google hit...)
    I've finally made it!! - I'm at the top of a Google search query return. Is there anything left to aspire to? ;-)
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