Good software to manage your readings for a PhD

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Wed Jan 13, 2010 2:54 pm Post

I'm a newby here, but was wondering if you could help me.
My university supports only Refworks - a software with which I don't go on too well - so I'm looking into other forms of software to manage my notes and references.

What I like to do with the software:
1. write a summary of what I've read - give it subject keyword(s) or tags that are searchable
2. write the reference
3. add a link to where the PDF or doc is saved on my computer (or on the web)
4. being able to search by author, title keyword, keywords or file type

Am not sure if Endnote can do this... I read good and bad stuff about it.

Any other useful tips,

Many thanks!

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Wed Jan 13, 2010 3:40 pm Post

EndNote can do pretty much anything you want and has the advantage of being cross platform Mac/Windows. My experience is the Mac version is buggy, although it's a while now since I used it, so it may well have improved. TBH I never really got on with it since it never seemed intuitive and, I always felt I was fighting it to make it do what I wanted. YMMV

Other bibliographic software on the Mac is Bookends and Senté Both of these will integrate well with Word, Mellel (especially Bookends) and Nisus.

There are 30 day trial versions of each, so it's probably best to give each one a run before you decide. All of them give academic discount.

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Wed Jan 13, 2010 4:23 pm Post

I'm using the freely available BibDesk, and I like it. Not as weel integrated with Mac wordprocessors like Sente of Bookends, but if you don't need "lively" updated references in your text, it works great.


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Wed Jan 13, 2010 5:29 pm Post

EndNote will perform all of the tasks you mention.
It works well with both Word and Pages.
I've never had problems with the Mac version.
The latest is Endnote X3.
If your campus has a license, it won't cost you much.

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Wed Jan 13, 2010 6:21 pm Post

You should definitely look at Zotero. The price is right, it seems unequaled in terms of the ease of getting sources into it, is cross platform, and it is being developed at a very fast pace. I use Bookends, which is wonderful, but for the price Zotero may be impossible to beat.

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Fri Jan 15, 2010 1:10 pm Post

thanks everybody. Will look into your suggestions. Zotero looks good since it's for free :-)

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Mon Feb 15, 2010 6:54 am Post

Also look at Papers - highly recommended ( (Assuming you are using a mac)

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Tue Feb 16, 2010 10:47 am Post

Papers is an interesting beast, because it doesn't actually format references as Bookends, Sente, and EndNote do. Its main claims to fame, in my view, are its very pleasant interface (including a full-screen PDF-viewing mode) and the fact that it has a corresponding iPhone/iPod touch (with an iPad version also planned) app, which allows you to carry around your references organized by your custom collections, by author, or by title, complete with PDFs attached.

A Bookends key feature, starting with the recently released version 11, is tag clouds. Sente has dynamite notetaking features.

Free reference management solutions include Mendeley and the already-referenced Zotero.

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Mon Feb 22, 2010 2:39 pm Post

I'm using Zotero with Scrivener. It lacks the nice integration that Bookends and Sente have within Scrivener but does a wealth of useful things in scraping references from webpages, bibliography, wordprocessor integration and web research with personal annotations. I write in Scrivener, placing my citations in curly brackets in the draft text (have defined a style for exactly this purpose in Zotero); the finished and exported rtf-file I'll then handle in NeoOffice after running Zotero's rtf-scan feature, which recognises my citations and produces the bibliography. It's a sweet set-up.

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Wed Feb 24, 2010 4:17 am Post

I use BibDesk and prefer it to Zotero b/c Firefox still doesn't use OS X context menus. I also had some problems getting Zotero linked files to sync across multiple computers (a few years back, last time I tried). It's free, has good web scraping and auto-filing capabilities, and with Applescripts available on the BibDesk wiki can be used pretty easily with any of the main OS X word processors.

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Tue Mar 09, 2010 2:30 am Post

Another program to look into is Mendeley. It's still a little shaky but it has some nice PDF annotation features. Plus it's free and cross-platform.

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Tue Mar 09, 2010 3:29 am Post

Mendeley's key feature is that there's a web version and desktop software for both Windows and Mac, with automatic syncing between them all. In a way, that means you don't have to choose between going all online for extreme portability and getting all the amenities of real Mac software.

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Fri Apr 27, 2012 11:40 pm Post

Sorry for raising a dead thread (I'm not sure how that's viewed here), but I want to put in another vote for Mendeley.

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Sat Apr 28, 2012 2:04 pm Post

CP, me old chuckle buttie,
Welcome aboard the leaky old tub, Scrivener. If you wanna raise the dead...then you go ahead and raise the dead! If any of the miscreants and bottom feeders on board Scriv object...then just flip 'em the bird. I'm not sure whether there's a keyboard short cut for it, but I'll check it out.
Image Once again, welcome aboard CP :wink:
Take care'
As a professional, you, are your one and only asset. Without integrity you are worthless, but with it, you are priceless.

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Thu Apr 25, 2013 7:14 pm Post

If ever there was a gap in the software, it is right here.
I know this blog was started ages ago, but it is a never ending story... :(

Mendeley is OK but does not pick up all the details required for correct citation - also just bought from Elvesvier which means it will probably start charging more and it is very much medically bias so lacking in other fields of study...the $$$ will make it not student friendly! :? :cry:

Refworks does not export/import so it means prior lists have to be put in manually - I have hundreds of citations so I am not willing to even start that one... Refworks was very inaccurate when I started using it 5 years ago, so I stopped... it might be better now. :shock:

I have a separate folder (about to have a separate project) in Scrivener for references - that I put in APA and Chicago - the two formats I use most, colour code if I need to double check it is correct... :lol:
and cut and paste as I need to use...

I then dropbox and references I might need when away from home :wink:

If anyone knows of anything else that has appeared please let me know