Klaas Wynne Klaas Wynne 3 May 2009


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Posted in Presentations quality, Technical (ms word, tex), Tips, useful software

When you are doing research, you tend to collect a lot of papers. I remember that at the end of m PhD, when I moved to another continent to do a postdoc, I dumped a huge box of photocopies in my parents’ basement. A few years ago, I had collected two cupboards full of photocopies. It was getting seriously out of hand. Then, of course, journals started putting everything online as PDFs and the same process started all over again but this time filling up hard disk folders instead. I used to have subject-based folders, which sort of worked until something fit within 2 or 3 or 4 of my subjects. Searching for some old paper you had read a few years back became more and more nightmarish. Then somebody showed me Papers.

Papers is a program that acts like your iTunes library for PDFs. It also connects to online search engines such as Web of Science (WoS), Scopus, PubMed, arXiv, JSTOR, Google scholar, and half a dozen other ones. That means that you can search from within Papers, retrieve, and store PDFs directly into your library but more importantly, Papers keeps a record of bibliometric data such as title, authors, abstract, doi, keywords, notes, etc. You can set up collections of papers by topic either by hand or by using smart folders that use automated searches of the bibliometric data. I like it that you can nest topic folders so you can either view PDFs from a sub-topic or go one level up to see all PDFs about that topic. My only complaint is the lack of Boolean and wildcard searches.

However, the best thing by far is the quick search function, which makes a real-time selection that narrows down as you type in more keywords. For example, you once read this paper, it was about X, one of the authors was Y, maybe it was published in Z. Once you type in X and Y, usually the selected list has narrowed down enough that you can see journal Z and a few seconds later the paper you were looking for. This is amazingly good! Last but not least, you can export all the data into an EndNote XML library (or BibTeX  etc.) and use it to make reference lists.

There is one tiny little problem: it only works on a Mac (or your iPhone but that’s not really that useful). The reason for this is that OS 10.5 has a PDF API built in (a subroutine library that can be used by any software) whereas MS is trying to push its own version of PDF. Personally, I was so hacked off with Windows Vista last year and so enamoured with Papers that I switched to the Mac. It’s the best decision I have made in a long while: I haven’t sworn at my computer since!

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  1. Unregistered

    3 May 2009 16:07, Dr Shock

    Now there you go. You should have switched before your thesis ;). I prefer sente for keeping my pdf’s because you can also use it for making references like endnote. It recognizes the articles very easily via pubmed or google scholar.
    Nice post, kind regards Dr Shock

  2. Klaas Wynne

    3 May 2009 17:39, Klaas Wynne

    Thanks W. Problem in experimental sciences is that you need to interface your computer to all sorts of equipment and then Windows rules. It’s easy to then get stuck with it. Glad I switched though.

  3. Jacopo Bertolotti

    6 May 2009 10:27, Jacopo Bertolotti

    I’m not going to switch to Mac just for using Papers (I feel fine with Linux) but I’d really love a similar program for any other platform. Searching for something useful I stumbled upon Sente and iPapers that both look a lot like Papers but are (sadly) also Mac-only programs. Going on searching I also found gPapers that looks promising (and run under Linux) but is still on a pre-Beta version, making it difficult to install and almost impossible to use.
    I have faith that, one day, it will work finely and I will be able to use it.
    Meanwhile maybe I’ll install MacOs in a virtual machine just to use Papers 😉

  4. Unregistered

    16 Aug 2009 9:09, David Stern

    I use a Mac and I just name all papers I download using the authors and date, e.g. Stern2009.pdf. The find function is so powerful on the Mac that it is very easy to find any of your papers either by file name or any content (doesn’t work of course for papers from JStor etc.) in them. No need for any extra software I think.

  5. Unregistered

    17 Aug 2009 8:36, Klaas Wynne

    Hi David. Papers also links to EndNote (and other bibliography generating software), which you couldn’t do with just Spotlight. Enough to make it worth the extra €29.

  6. Unregistered

    23 Aug 2009 7:57, Gene Dog

    EndNote is also powerful to manage papers.

  7. Unregistered

    28 Aug 2009 6:44, Snaptastic

    I can’t believe no one has mentioned Mendeley. Just like papers except they support windows, linux and mac. It has every feature you mentioned about papers and they are very active in adding/improving features.

  8. Jacopo Bertolotti

    28 Aug 2009 14:23, Jacopo Bertolotti

    @Snaptastic: personally I didn’t mention Mendeley because I didn’t know about it but, after reading your comment, I searched a bit on the net and I installed it. In the next days I’m going to test it and let’s hope it is as good as it seems to be 😉

  9. Unregistered

    12 Dec 2010 15:22, Sanjay Singh

    Hi Klass
    Thanks a lot for pointing to Papers. May I request you to tell some free tools just like Papers and which can run on windows also?

  10. Klaas Wynne

    14 Dec 2010 17:04, Klaas Wynne

    @Sanjay: Unfortunately for you, Papers is not free. There is a similar program for Windows called Mendeley and it is also not free. As the Calvinistic Dutch say: only the sun rises for free…

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