31 replies to this topic

[esquila]

Hi everyone,

I've been thinking about my software choices--free and paid apps--and I'm wondering what the hive mind has to say about it. Specifically, what are your favorite ways of organizing citations and pdfs? Do you have any favorite project management software?

Any other personal favorites? By all means, wax poetic!

[contretemps]

Zotero!

[Delarosa]

My university library supports and encourages use of RefWorks and Write-N-Cite, but I'm not partial to 'em. I'm going to try Zotero for the upcoming academic year.

[Eigen]

Endnote.

By far the most robust citation software I've tried, and also one of the most widely used. I will, however, recommend that in the sciences, you use what the rest of your research group/advisor use. That gives you easy imports of their citation libraries, and makes co-writing papers a heck of a lot easier.

For data plotting, Origin is what I use, although I'm thinking about trying out Prism.

For writing, Scrivener is great for getting thoughts on paper, but I end up doing most of my actual compiling in Word still (again, it's what other people use).

For everything, a full copy of Adobe is a godsend. Managing almost everything in PDFs is really easy with it.

For figures, I make most of mine (painstakingly) in Illustrator- CS5 has a lot of nice upgrades over CS4, imo.

Otherwise, see what your department provides, and your advisor/labmates use.

Edited by Eigen, 13 April 2012 - 04:59 PM.

[Behavioral]

TIL about Scrivener.

That's $40 of my research budget well-spent, I must say.

[Eigen]

Heh, I'm actually still on the 30 day free trial. It's one of the best 30 day trials I've used... It actually counts down 30 days of use, not 30 days since registering.

[Behavioral]

Well, that's awesome. I wonder what the backend programming is and whether it's susceptible to freezing your computer's date/time.

Regardless, I watched the video demo and it was basically a streamlined version of everything I already do. When I write a manuscript, I definitely develop my ideas in blocks that may or may not be related to each other, and I edit/arrange everything once I'm done writing. This means I have a dozen of .doc files with a section or a few paragraphs that I have to open at once to begin the stitching-together process. The demonstration was literally everything I've wanted in a writing platform for years.

I should get paid for shilling their product.

[esquila]

This is getting interesting! It's fun to see what everyone else uses.

I'm messing around with Scrivener now, too. It seems great, and I think I'll stick with it, but ultimately I'm going to compile things in Word (always have, and as you say, Eigen, everyone else does.)

I've always used EndNote, but a friend of mine mentioned Papers to me, and it looked good. Sadly the functionality isn't nearly as good for Windows yet. (If it does get as good as the Mac version, I'm definitely going to switch to Papers from EndNote.)

For graphing and data analysis I mostly use IgorPro, but in the very near future I'm going to need to start using MATLAB for some things. Even when that happens, I'll probably still do a lot of work in Igor. Thankfully I get both free through my university. I use Adobe Illustrator for line drawings (they come out decent, but take forever). I'm not averse to using MS PowerPoint for quick drawings either... the drawing tools have gotten much better, even if the program isn't exactly what I would hope for in a presentation maker.

Also-- Dropbox and GoogleDocs. Dropbox is how I share papers and data with my advisor and collaborators, GoogleDocs is how I write manuscripts with collaborators.

[msafiri]

I used to use EndNote but then switched to Zotero, rather than upgrading to the newest version of EndNote. Otherwise, I can't say that I use any specialized software really... Just MS Word/OpenOffice, PowerPoint/Impress, notepad, etc. Oh, I used to use Post-It Notes for the computer but, I stopped when I started using my netbook more often because it made the screen too cluttered. I did feel more organized when I had it though.

[go3187]

I use Mendeley for organizing and reading papers, and (mostly) IDL for programming and plotting. I write my papers in kwrite, using Latex, and then ps/pdf them from the terminal. (I work in Linux.)

[Dal PhDer]

For PDF editing and notes, I like PDF X-Change. I like the ability to highlight and take notes even on locked documents- and it's free.

I have not really been accepting of Reference programs. However, I have begun using RefWords just because it's free through my university. I am actually surprised at how much easier it makes things and was sadly disappointed that I was resistant for so long.

I also like the program called XMind for mapping out projects and papers.

Prezi is a great free presentation creator. There is a learning curve, but it's a really neat way to deliver presentations and engaging lectures (especially to students).

This is a great thread- it's always great to see how other students organize their work and what they find helpful!

[Delarosa]

I'll just add Freemind for mind-mapping and FocusWriter for a no-nonsense text-on-a-background no-bells-or-whistles distraction-free writing program. Both are free programs (available through the Software Centre if you're using Ubuntu).

[MaxiJaz]

I use Mendeley for organizing and reading papers, and (mostly) IDL for programming and plotting. I write my papers in kwrite, using Latex, and then ps/pdf them from the terminal. (I work in Linux.)

Thanks for the Mendelay recommendation. I'm using it on Ubuntu and it works swell! Oh how I feel so stupid keeping separate folders of my pdf's and google doc backups after all this time. I haven't used it as a refworks replacement...thoughts?

Edited by MaxiJaz, 15 April 2012 - 07:53 PM.

[MaxiJaz]

In reference to my post above, I found this to be useful, but keep in mind that it may be biased: http://www.mendeley....mpare-mendeley/

[Eigen]

I have to say, that list is horribly biased to the point of being blatantly incorrect, from a perspective of Mendeley vs. Endnote. And I don't think it's updated to include features from the current version (X5) of Endnote.

Similarly, a lot of the points are phrased just so that it knocks another "out", when a slight tweak would make it a feature one of the others have.

[MaxiJaz]

Can't say I didn't warn you. I didn't really use the list to make my decision, I'm type to try whatever I have available and make my decision after that, but the list was helpful in letting me know what I can and cannot do.

[Eigen]

I guess that was my point, there are lots of things that several of the programs are listed as not being able to do that they can.

But my post was more to anyone else that reads it looking for a decent comparison between the two.

Here is a nice comparison of a lot of different packages.

Edited by Eigen, 19 April 2012 - 02:00 AM.

[go3187]

Thanks for the Mendelay recommendation. I'm using it on Ubuntu and it works swell! Oh how I feel so stupid keeping separate folders of my pdf's and google doc backups after all this time. I haven't used it as a refworks replacement...thoughts?

RefWorks is the software provided by our university, but I haven't tried it. I started with Mendeley, and sticked to it just because I'm a creature of habit.

However, for my field and my way of working, Mendeley does everything I need. I mostly use it to save trees by not printing every paper I'm interested in. I like that you can highlight stuff you're interested in, add notes, and then share the annotated files with collaborators.

I'm not sure how it works in other fields, but in astrophysics we can find essentially any paper here: http://adsabs.harvard.edu/, and the site allows one to download a bibtex entry for each paper. So I get all the bibtex entries I need from this website, and (gasp!) have one BIG text file in which I save all of them. I write my paper in latex, using kwrite. I remember when I was writing my 3rd paper, I emailed the tex and bib files to my advisor, and he commented that there were many references in my bib file which I didn't need for the paper. He was shocked when I told him I use one common bib file for all my papers, lol. It's probably not the most organized way of handling references, but so far it's been working fine for me.

[Behavioral]

I use EndNote and have different folders for my bib files, which I use for my different programs of research. I can just select all the citations from one of my folders and use "Copy Formatted" to create a document in Lyx (I'm not as hardcore as you true LaTeX nerds!) instead of having one giant bib file that doesn't differentiate between my Paper A and Paper B citations.

[MaxiJaz]

I guess that was my point, there are lots of things that several of the programs are listed as not being able to do that they can.

But my post was more to anyone else that reads it looking for a decent comparison between the two.

Here is a nice comparison of a lot of different packages.

Eigen, just curious, but do you use Endnote at home? I've only been able to use licensed versions of it on campus computers, but the software is awfully pricey.