SDN members see fewer ads and full resolution images. Join our non-profit community!

Reference Software/Archiving Software for papers

Discussion in 'Physician Scientists' started by Harlow, May 10, 2008.

  1. Harlow

    Harlow 7+ Year Member

    Sep 18, 2007
    So in reading advice and getting feedback from current students, I've decided that it's probably in my best interest to make a go at getting more organized. Anyone have any preferences on software to organize journal articles?

    My ideal program would be something that can organize saved PDFs of articles as well something that makes for easy referencing when I'm writing.

    I've been messing around with bibus recently, but wanted to see what everyone else uses.
  2. SDN Members don't see this ad. About the ads.
  3. linuxizer

    linuxizer MS0 10+ Year Member

    Jul 31, 2003
    CiteULike is pretty good, has some nice social features, and can be accessed from anywhere, so if you see a good paper at a conference or whatever you can add it. When you're ready to write you can export a bibliography to EndNote or BibTeX or whatnot so that you can cite it easily in your papers. And it lets you tag your references with words so that you are categorizing as you go. Also lets you store a PDF with the article (only you can access it, so they get around copyright complications that way).

  4. meowkat444

    meowkat444 10+ Year Member

    Mar 10, 2007
  5. PBandJ

    PBandJ hot dog back in action! Moderator Emeritus 10+ Year Member

    papers is great if you use a mac.
  6. redoc

    redoc 2+ Year Member

    Nov 3, 2007
    Reference Manager



    Both are compatible with pubmed and other ejournal sites
  7. kapMD/PhD

    kapMD/PhD T-1 yr 7+ Year Member

    Jul 25, 2005
    so Mac Users- i just got a mac and need a reference manager of sorts to start the dissertation work. Is "Papers" what everyone uses or are there other options? I'm new to this, so any suggestions are welcomed. Thanks!
  8. grendelsdragon

    grendelsdragon Synesthetic 2+ Year Member

    Jul 28, 2007
    EndNote is pretty much the standard in academics.
  9. Maxprime

    Maxprime Higgs chaser 5+ Year Member

    Nov 28, 2005
    +1 to EndNote - will save you hours upon hours. When space is short in grants, you can use numbers for notations and as you go back and insert references EndNote will automatically fix your numbers to reflect the changes.

    Use the "Connect" function to jump onto the NLM and you can search by the PMID, then right click and save your PDF - easy as that.
  10. GWD

    GWD 5+ Year Member

    Aug 30, 2007
    Endnote. //end thread

    The "cite while you write" function is invaluable.
  11. totipocincy

    totipocincy Member 7+ Year Member

    Apr 15, 2008
    I used Endnote all through grad school, and for the most part it worked well as described by others in this thread. However, there were many new versions released and they weren't always seamless from one to the other, particularly across platforms (MAC - PC). I use a web-based application now with all of the features of Endnote, but without the headaches. RefWorks is available at my institution, and has been great. Multiple users can access libraries online, you can store pdf's there, as well as easily import Pubmed refs and create bibliographies. The interface isn't as pretty as Endnotes, but it is much more convenient.
  12. grendelsdragon

    grendelsdragon Synesthetic 2+ Year Member

    Jul 28, 2007
    When using EndNote with a manuscript that is to be shared with coauthors or colleagues, I always recommend sending a document where the "remove citations" has been performed, with all citations delimited by special characters. This ensures compatibility between versions of EndNote software and between operating system platforms (Mac OSX, Windows XP or Vista, and Linux).

    Also remember that the "remove field codes" has to be performed before submission to most journals.
  13. jsg1985

    jsg1985 2+ Year Member

    Jan 11, 2008
    Gaithersburg, MD
    End note for reference for sure.

    For everyday scientific reading, I use paper and skm. I do like to organize and back up my articles using Paper (Mac only). I use Skim to annotate the PDFs.
  14. czarrar

    czarrar 2+ Year Member

    May 20, 2008
    I just started using papers and it is excellent. However, it is still new and there are some features that are not well developed (e.g. creating bibliographies) and there are several bugs. Taking that into account with the fact that I think the developers intended it to be used along with more heavy duty citation software, I would recommend using papers in conjunction with endnote. Alternatives to endnote on the mac include sente, bookends, and bibdesk.

  15. schrizto

    schrizto 2+ Year Member

    May 14, 2008
    puh puh pitt
    hSDN Alumni
  16. Martin1982

    Martin1982 Banned

    Aug 18, 2009
    Hey, my university subscribes to Endnote. It is not bad, though it will take some time for you to learn how to use. Recently, someone introduced WizFolio in my school too. I think it is pretty good. You can sign up for a free account and give it a try.
  17. Indoctorate


    Mar 7, 2011
    Mendeley seems to be becoming the next big piece of software for postgraduates. I've written a review of it if you would like to see some opinions from different students and my own take on it.

    If I was to summarise it, it is basically like iTunes for geeks :thumbup:
  18. rgejman


    Apr 18, 2010
  19. achamess

    achamess 7+ Year Member

    Jul 6, 2007
    Looks pretty awesome :)
  20. vc7777

    vc7777 Nontrad MD/MS Resident Rocket Scientist Physician Moderator Emeritus 7+ Year Member

    Jul 1, 2009
    Another vote for zotero - webbased and actually pretty slick

    Not sent from my cell phone :shifty:
  21. dreamsofspring

    dreamsofspring on a roll

    Feb 4, 2008
    I use Sente for my mac. It's great and syncs really well with Mellel, which is an academic word processor with 1/100 the problems of Word.
  22. fozzy40

    fozzy40 Senior Member 10+ Year Member

    Jul 7, 2001
    Portland, OR
    Anyone use Mendeley?
  23. PBandJ

    PBandJ hot dog back in action! Moderator Emeritus 10+ Year Member

    I've bounced around between refworks and mendeley and now I use mendeley almost exclusively. It's great for being able to sync your papers between your computer and your mendeley web account (meaning that you can access any papers from other computers anywhere as long as you have an internet connection). You can add notes and highlights to papers as you read them, you can organize your library nicely, and it's nicely integrated for direct citations in microsoft word if you want.
  24. Swammerdam

    Swammerdam 5+ Year Member

    Aug 9, 2011
    I use Mendeley. I think it's awesome, and way better than endnote. Plus it's free!
  25. JustForPretend


    Jun 17, 2011
    +1 for Zotero
  26. fozzy40

    fozzy40 Senior Member 10+ Year Member

    Jul 7, 2001
    Portland, OR
    Currently, I use Zotero with Dropbox and iAnnotate since I read off of my iPad. I also use Mendeley to sync with my Zotero account for back up.
  27. Chimneysweep

    Chimneysweep 5+ Year Member

    Oct 16, 2009
    FYI, Papers2 has similar functionality to EndNote.
  28. erikreinertsen

    erikreinertsen MD/PhD student 5+ Year Member

    Aug 18, 2009
    Atlanta, GA
    I absolutely love and highly recommend Mendeley. I'm an advisor which just means I tell all my friends about it but let me know if you have any questions (or anyone else here, I think we're all pretty knowledgeable based on the posts).

Share This Page