Favorite software?

[MaxiJaz]

I use both Mendeley and Zotero, between them they have most if not all the functions I need. I'm a fan of good open source software that stops me giving more money to either Apple or Microsoft. I use PDF Xchange instead of adobe and GIMP and Inkscape for any image working that needs to do. I also use audacity for transcriptions.

I also do a lot of group work so dropbox is fairly essential, though I have Ubuntu One and Box too for extra backup.

They all cost me nothing.

wooohoo open source!

[TakeruK]

I'm also a Mendeley user! My supervisor is old fashioned enough (I am programming in a standard that's 10 years older than me) that he does not use any of these fancy new software so I guess I can use whatever I want If we are discussing a paper, he would pull out his file cabinet and somehow find exactly which folder it's in and hand me a copy! It's impressive but I prefer my more-green approach and only print out the more important stuff haha.

I like Mendeley because of its dropbox-like feature. I have it installed on my work computer, my work laptop, and my home/personal PC, so I never have to worry about sending myself PDFs, or managing files on a USB key etc. I also never have to worry about creating a logical/easy to find folder structure to store all the PDFs (and not to mention naming every file some standard way), because like iTunes does for my music, Mendeley does for my papers! It also allows me to create a search/sort of database and sort my papers by year, author, journal, tags that I create myself, keywords, etc. I also like its BibTeX export feature -- now I also don't have to worry about formatting bibliography entries too much either. I use the ability to annotate/highlight and organize PDFs for both papers as well as online/electronic course notes. And finally, it's all free!

I'm not sure if Mendeley is the best software out there, but I remember hearing about Papers before grad school but didn't have reason to buy it. When I started, someone mentioned that Mendeley is basically a free version of Papers, so I went for it! I'm happy to switch to another software as long as I can still do all of the above, if my PhD research group uses something else! So while Mendeley is great and fits my needs, I don't think there's anything so amazing about it that I wouldn't want to leave.

[Done]

Although having licenses for EndNote etc. the best thing i ever did was switching to Latex, especially because I often need to use math operations in my works.

The two good things about latex are, that I can define my on style and latex will do the rest for me and secondly I can just put all quotes in a big txt file, where I can put in the data I need/want.

[virion]

For any biologists using MS Word 2007 or later, the following plugin is pretty great: http://compbio.umbc.edu/3655/ (DNA/Protein sequence related)

Edited June 22, 2012 by virion

[Dal PhDer]

So I have used this thread as my go to "what do I need to help me" ... and I am going to be honest...I used Mendeley a few years ago and thought it blew- like... most useless program EVER....but I decided that I would try it out again since many of you recommended it.... oh.my.....I LOVE IT!! Seriously!! Annotations, access to any of my computers (PC at home, Mac laptop, PC at work)...seriously....I want to marry this program!!! MARRY!

Please guys- keep the recommendations coming!

[fuzzylogician]

There's a long thread from a couple of years ago that could be useful:

I've recently started using a note-taking app called WorkFlowy (read about it here), and I LOVE it. I'm a list person and have tried many apps, and this one really does a good job organizing all my lists while keeping the design clean and simple.

[Dal PhDer]

Thank you fuzzy!! Both for the thread and the suggestion!!

My desktop is filled are so filled with post-its that the program has become useless! WorkFlowy looks amazing...i like how it can be both a simple list program, but also a great mindmapping tool! I will have to check it out!