Harlow

10+ Year Member
7+ Year Member
Sep 18, 2007
17
0
Status
MD/PhD Student
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.
 

linuxizer

MS0
10+ Year Member
15+ Year Member
Jul 31, 2003
276
0
Visit site
Status
MD/PhD Student
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).

Ari
 

redoc

10+ Year Member
Nov 3, 2007
52
0
Status
MD/PhD Student
Reference Manager

or

Endnote

Both are compatible with pubmed and other ejournal sites
 

kapMD/PhD

T-1 yr
10+ Year Member
7+ Year Member
Jul 25, 2005
140
3
PA
Status
Resident [Any Field]
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!
 

Maxprime

Higgs chaser
10+ Year Member
5+ Year Member
Nov 28, 2005
2,125
7
Status
Medical Student
+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.
 

totipocincy

Member
10+ Year Member
7+ Year Member
Apr 15, 2008
15
0
Status
MD/PhD Student
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.
 

grendelsdragon

Synesthetic
10+ Year Member
Jul 28, 2007
95
1
Status
Attending Physician
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.
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.
 

jsg1985

10+ Year Member
Jan 11, 2008
10
0
Gaithersburg, MD
Status
Post Doc
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.
 

czarrar

10+ Year Member
May 20, 2008
11
0
Status
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!
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.

Cheers
 

Martin1982

Removed
Aug 19, 2009
1
0
Status
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.
 

vc7777

Nontrad MD/MS Resident
Moderator Emeritus
7+ Year Member
Jul 1, 2009
3,568
280
Midwest
Status
Resident [Any Field]
Another vote for zotero - webbased and actually pretty slick

Not sent from my cell phone :shifty:
 

dreamsofspring

on a roll
10+ Year Member
Feb 4, 2008
8
0
Status
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.
 

PBandJ

hot dog back in action!
Moderator Emeritus
10+ Year Member
Aug 25, 2005
5,521
5
toast or english muffins
Status
MD/PhD Student
Anyone use Mendeley?
Fozzy,
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.
 

Swammerdam

5+ Year Member
Aug 9, 2011
13
0
Status
Medical Student
I use Mendeley. I think it's awesome, and way better than endnote. Plus it's free!
 

erikreinertsen

MD/PhD student
5+ Year Member
Aug 19, 2009
95
1
Atlanta, GA
erikreinertsen.com
Status
MD/PhD Student
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).