I am also using JabRef since a long time, it works perfectly well. Recently I found that literature from scholar.google.com can be exported to BibTex, which can then be imported into JabRef since BibTex is JabRefs native format.

Mendeley seems easier for reference import from endnote than Jabref but it doesn't have very many styles and none that I usually use. Do you custom make styles everytime you publish in a different journal?

It depends on the word processor you are using for your papers. If its Tex, you can use JabRef's BibTex database along with appropriate style files which are provided by many journals, see

http://en.wikipedia.org/wiki/BibTeX#Style_files

If you use OpenOffice or LibreOffice instead, you can use JabRef's OOffice plugin which also provides some style files which can be easily modified if required, see

http://jabref.sourceforge.net/OOPlugin-jabref.php

What about Bibus or Zotero? Also see Wikipedia [1]. Myself I use bibtex (bibliography management for LaTeX).

Edit: now I am also using Zotero.

[1] http://en.wikipedia.org/wiki/Comparison_of_reference_management_software

Thank you all very much for your helpful comments. I'll try the different options and come back to you.

Anyne know of a non-web based alternative?

You can try Jabref bibliography manager

I have tried Zotero; the fact that it is tied to the browser makes it rather difficult to use, in my experience (which mkay be due to my own lack of expertise/understanding). I like the way Mendeley works, but have trouble with how Mendeley automatically records citations for documents I have stored locally, with no way to edit the citation manually that I have been able to figure out.

What I like about Mendeley is that I can do all of my research on a single platform- break research up into projects, have a localized list of the documents I am currently working with, annotation, and highlighting are easy to use, and I can create my working document within the same environment. Mendeley, however, was designed to be web-based, for collaborative work, and seems to lack the flexibility (i.e., ability to correct the erroneous citation information manually).

Most of my research is not intended to be published, although it occasionally results in something worth sharing. I do it as a hobby. On the other hand, the wife is a lawyer, and I can see some real application for her work with something like Mendeley.

Jabref seems to be only a mangement tool for building a bibliography. Mandeley and Zotero offer functions for capturing my thoughts while reading the documents, tying them to the source material.

A major problem I have with web-based approaches is that links to on-line resources are not always stable. Try recovering a document you discovered a couple of years ago. All to frequently, the original link no longer works, and the search effort has to begin all over again. Not all documents are in the public domain- if one has purchased the reference material, trying to link to a web copy is not going to work. If the citation is not recorded properly and one eventually publishes the work, others are going to have trouble following the trail...

Zettlekasten looks very promising, but I am a bit concerned about it being Java-based- especially since it requires the "Official" Java 6 rather than the Open Source Java. I am not sure this still applies, since Sun Java no longer exists- it is now Oracle Java...

LitLink looks promising, and older versions appear to have been tested with Wine, with some issues- pretty dated test results. It might be worth testing in VirtualBox, but right now I am limited to Win 98SE in my VirtualBox installation, and LitLink wants XP or later. Also, I suspect my German is a bit too rusty to handle the documentation...

I will have a look at both of these programs in the near future...Thank you.

Zotero is easy to use an integrates well with online research. Plugins for openoffice/libreoffice/word give additional benefit. Some overly complicated citation styles are not handles by Zotero though.

I can not recommend bibus.

Short answer: use JabRef. Nothing better, IMHO.

Pybliography : http://pybliographer.org/

Mendeley: http://www.mendeley.com/

Consider BibDesk (If you are a MAC OS X user).

Nico-

This Cilavi software looks more like what I am after- unfortunately, it seems to be Windows only...I will give it a try in Wine.

I just came across Mindraider (http://mindraider.sourceforge.net/), which is more along the lines of what I am looking for with regards to organizing a research project, but I am not sure of the citation formating capabilities as yet- haven't had sufficient time to work with it. Seems to provide a platform to consolidating references, notes, ideas, etc.

Hailey-

I prefer something not tied to the browser...

What about Mendeley (http://www.mendeley.com) ? For me, it works fine. Have a stand alone version with synchronization options on web database and web version as well.

I have been using Mendeley, but have a couple of issues with Mendeley. Primarily, I haven't been able to figure out how to manually edit a citation- sometimes, the automatic citation gets the details wrong (i.e., recording a completely unrelated Journal as the source of the document- in some cases, even recording the Author incorrectly), and the only way I have figured out how to correct this is to delete the citation and start over- apparently no way to correct the information manually.

Secondly, Mendeley is document-centered- easy to make notes, highlight important concepts, etc. within a document, but not so easily oriented toward a research topic. For instance, in Zim, it is easy to link documents to my own "working paper"- i.e., the scratch pad I use to generate ideas, describe processes I am experimenting with, etc. So far, I find Zim easier for organizing my own thoughts while Menedeley is handy for making notes while reading. However, Zim tends to hang when one links to excessively large files.

Zotero was the first application I used- my problem with Zotero being browser-based is speed.

OK. I don´t know Zim, yet, and Zotero as well. I tried EndNote and Mendeley.

About Mendeley, I will try to help a little more.

Sometimes doesn't work fine with automatic citation? Yes, I think so, but nowadays is possible update information manually. Just click on the field with the information that you want to update and type the correct form.

I liked your explanation about how to Zim can links documents to "working papers" and the feature to take notes about ideas, process, etc...

Have you heard of Citavi? It helps you to organize your research in many ways: obviously there are notes and references which you can easily insert into whatever you're writing. It manages quotes, thoughts and summaries. If you have a source saved on your computer as a .pdf file, Citavi will include this in a small reading screen so don't need to open the adobe reader.

There are two versions, one is free of charge but only allows you to include 100 titles in your bibliography. The pro version is about €100 and you can include as much literature as you like, work in teams, manage an endless number of projects.

Citavi is Windows only- Wine Appdb provides mixed results, with some work arounds, and one could possibly use this in a virtual guest, but I would prefer something native Linux. Coming out of Europe, I am surprised they do not offer a native Linux version.

Charles, I have no problem editing citations in Mendeley. Just click on the article in the program (not when inputting into Word) and change the details (list on the right). I find that the software gets the citation right about 60% of the time during the inputting process and almost never when I have an inter-library loan article. So building the database is rather annoying; however, once built though it seems to do a pretty good job.

You can also change the citation styles, but unfortunately this is not quite as intuitive as it should be. It requires modifying some code. If you do some google searches, you should be able to find some examples.

I know about editing the citation when I first add a reference to the library in Mendeley, but sometimes I am in a hurry and don't pay a whole lot of attention to the entries. On occasion, I have had to delete the reference from the library and re-import, because the later changes don't always take...An aggravation, not a show-stopper.

I am pretty sure you can still edit it after first importing it; however, I agree with your frustration in that it is probably easier to reimport the file/paper. I find most citation software to be rather tedious to initially set-up. Mendeley is probably one of the better ones at it (although far from perfect).

...you can try Litlink. It´s open source. An overview you´ll get on the second link from the university of zurich

http://www.lit-link.ch/

http://www.id.uzh.ch/dl/sw/angebote/lit/Overwiew.html

If you need a non-social networking tool for bibliography then use JabRef (http://jabref.sourceforge.net/) or on OSX use BibDesk (http://bibdesk.sourceforge.net/).

Mendeley and zotero ;o)

We need just numbering of references in publications. For this purpose Neooffice is used. However, it is running on MACs only. I assume OpenOffice is comparable to that.

An update on my experiences to date. Bear in mind, I am more concerned with keeping a personal record of my sources than generating a formal bibliography for publication, and I use Linux. However, I recently encountered a situation where I wanted to generate a bibliography for sharing with someone else, and I used Mendeley. While the issues I encountered may be related to a lack of experience with this sort of activity, I found that I had to hand-edit the resulting bibliography extensively, especially where multiple authors were listed, and Internet links did not come out as I expected. I am not sure that my final result would comply with conventional "standard" formats. Mendeley seems to be a nice tool for reading documents and annotating them for future return to key information.

With regards to organizing my own research, I find that Zim Desktop conforms to my personal needs quite nicely (except that, it tends to get a little unstable when one attaches too many large files- better to link to references than attach them), or KNIME, which was developed as a data analysis tool, more than a general literature research tool (depends on what I am doing as to which I would prefer). I haven't had the need as yet to attempt generating a formal bibliography from either of these as yet.

I find Zotero a little awkward and slow, because of the browser interface- I haven't tried the stand-alone version yet.

Citavi looks very interesting, but, unfortunately, appears to be Windows only. Hard to do serious work in a Windows environment...

I would recommend Mendeley. It is great!

Http://www.mendeley.com. This is the link

I am using Zotero and I am happy with it. It is worth watching the video tour: http://www.zotero.org/support/quick_start_guide

I have tried a whole bunch (Zotero, JabRef, various BibTeX managers, Sente [for OSX; not free]] and finally converged to Mendeley, It does a pretty decent job and (importantly for me) works in Linux, OSX and Windows. It can export various formats (incl BibTeX) and there are a plugins for LibreOffice and Word. I have a few thousand references and Mendeley is able to handle them nicely.

Mendeley seems to be the best so far, despite the fact that it lack some functionalities.

I have set up a website which talks about software in the social science research. It will be completed the next days and you can find any kind of software which is or can be used explicitly in the research process. Enjoy.

http://www.sosciso.de

Here in our team we are also using Mendeley for sharing publications. Unfortunately not all members are using it yet and it lacks some important features (e.g. sharing of notes and highlighting in pdfs, better tuning of the bibtex output, more free storage space, etc.) which would help us to make our research more efficient. But I agree to the others here, Mendeley is so far the best platform and application to use as an open and free alternative to Endnote.

In terms of reference management++ you should also consider Docear which is under heavy development as it seems. They use JabRef as their reference management and add additional features like creating mind maps, projects and the like. And, sorry to correct you Jens, this software is purely free, not like Mendeley which is limited in space....

http://www.docear.org/

The fact of Elsevier being the new owner is a good new?

Oh, sorry. Sometimes is difficult to get the sarcasm when written.

It´s not exactly open source but i can recommend papers2. You can export endnote files and load it into papers2. For me it is the easiest way to manage papers, books and web articles with the added feature of searching all major scientific search engines such as pubmed. The price is relatively low for what you get for it. Over the past couple years I tested a couple free and paid products in that field and papers2 is second to none.

Check this

http://alternativeto.net/software/endnote/?license=free

Take a look at Bibdesk (http://bibdesk.sourceforge.net/). It is free, open source, and pretty powerful.

Hi,

I want to share with you this comparison table (between EndNote Web and Zotero):

http://guides.lib.purdue.edu/content.php?pid=150492&sid=1283473

...it depends for which reason I´m using a tool. Litlink from Switzerland is for some reasons a nice tool to and doesn´t cost you anything

Udo, the software looks promising. Is the website just available in German?

@Udo, hehehehe. No, I just speak English and Spanish (I used Google Translate).

I have found some tools that are really useful, like Zim for taking notes (the main problem is that I couldn't fix the LaTeX plugin for Windows).

i would recommend Docear which I am developing :-) It's free, open source, available for Mac OS, Windows, and Linux, and has a very unique concept to manage academic literature (in particular PDFs and annotations).

http://www.docear.org/2013/10/17/docear-1-0-stable-a-new-video-new-manual-new-homepage-new-details-page/

I add to the discussion this 2 posts from Docear's website:

http://www.docear.org/2014/01/15/comprehensive-comparison-of-reference-managers-mendeley-vs-zotero-vs-docear/

http://www.docear.org/2013/10/14/what-makes-a-bad-reference-manager

Really good indeed,

Nicolas

And option that I found missing in most of the apps is a version for Android (a Tablet could be really useful for reading/annotating pdfs), except for: Qigga and Colwiz.

if you are interested in a comparison of Mendeley and Zotero (and Docear), our new in-depth review might be interesting http://www.docear.org/2014/01/15/comprehensive-comparison-of-reference-managers-mendeley-vs-zotero-vs-docear/

Hi Joeran,

Actually that was the link that I shared before. And I should say that you did a good job right there. I would also recommend the other post about what makes a bad reference manager.

Thanks Joeran. This was useful.

I tried Docear but found it very difficult to get the hand of it. Did not have a lot of time to get in depth so with more effort, I would see the benefits. With Mendeley I am a bit scared of the bugs in BibTex export that you mention in your review.

I use Zotero and couldn't be happier. 

I am a linux user, and i work with Mendeley without problem

I highly recommend Auratikum (https://auratikum.de). It is a full integration of Niklas Luhmanns note-box-system (Zettelkastenmethode), works on all systems (webapplication) and gives order to your sources and list of contents.

EDIT: Auratikum is right now available only in german. (English in planning)

Well, the website for Auratikum is just in German

Dear Nicolas,

your are absolutly right. I should have mentioned that and edited my initial comment. Sorry for the confusion!

I use Zotero and find it very practical notably for word documents. You have just to click on a web page describing a paper to automatically save it in your bibliography. Your bibliography is easily updated and can be used on different computers. When i was looking for such a software, I found Zotero free. Is Mendeley also free?

I use bookends (https://www.sonnysoftware.com) and it is very promising. Though it is not free but worth paying the price. For writing paper, i use scrivener but i find even the manuscripts.app also very nice. Though it is a bit buggy.

What a useful thread. I'm left with the doubt though: which has more default and built-in references styles; Mendeley or JabRef?

Also, my first attempt at importing my Endnote database was successful but as the first post of this whole thread noted, it didn't work perfectly. Namely, the publishers of all of my book references were left out. Anyone know a fix to that?

Help on both counts would be much appreciated!

Alternatives to EndNote for all platforms with Free License:

https://alternativeto.net/software/endnote/?license=free

Have you tried Zotero. It offers a Browser version as well as a desktop stand alone version. Both are very good.