Mac and web apps to help keep a science grad student organized.
March 10, 2010 9:10 AM   Subscribe

I’m starting grad school in chemistry in a few months and I am looking for Mac/web apps that are useful to help keep a science grad student organized…citations, notations on papers, brainstorming, etc. Any ideas?
posted by stevechemist to Education (26 answers total) 23 users marked this as a favorite
EndNote is pretty highly regarded in the science fields. I tried it in law school without success, but I think that's largely because legal citation format is...nonstandard.
posted by devinemissk at 9:13 AM on March 10, 2010


Best, bar none.
posted by TheOtherGuy at 9:13 AM on March 10, 2010 [1 favorite] I know that a lot of the local program versions are probably sleeker, but as a grad student, sometimes it's easier to just be able to get all your citations anywhere. And I don't know that anything else does such a nice job of grabbing the citation information for you. (I'd be happy to be corrected on that one.)
posted by ansate at 9:20 AM on March 10, 2010

Brainstorming: Dokuwiki (plus plugins; see diagram plugins for example). I like the minimalism theme, as the default theme is a bit crowded.
posted by circular at 9:25 AM on March 10, 2010

I probably should have linked to chemistry plugins for you when I mentioned dokuwiki...
posted by circular at 9:28 AM on March 10, 2010

For organization/notes, Evernote.

For citation/PDF organization/Research: Zotero.

Although the above mentioned Papers looks amazing.
posted by griffey at 9:30 AM on March 10, 2010

For all your Papers-y needs, but free, and with the online-access goodness of Citeulike: Mendeley. Best thing of its kind I've seen.

Also, I don't know if LaTeX is a boon for chemists like it is for math/computer people, but I'm rather in love with LyX as a front end for that.
posted by Schlimmbesserung at 9:39 AM on March 10, 2010

If you use LaTeX on a Linux-flavored system, Kile is a pretty great front-end. If Mac-based, I'm a fan of TeXShop with Bibdesk for BibTeX organization.
posted by PMdixon at 9:42 AM on March 10, 2010

Ditto on Mendeley.
posted by quodlibet at 9:47 AM on March 10, 2010

Should mention Wyneken too, just because you'll hear about latex...

If you've been wanting the benefits of LaTeX or an advanced document system but don't want to deal with a steep learning curve, give wyneken a shot.
posted by circular at 9:49 AM on March 10, 2010

I really like RefWorks, which is an online reference management system offered through my institution.

Also, if you do any microscopy, you should check out ImageJ.
posted by beepbeepboopboop at 10:21 AM on March 10, 2010

I use Mendeley as well. I haven't used it on Mac, but after trying a couple of different similar systems, it worked the best for me.
posted by demiurge at 10:21 AM on March 10, 2010

for cool presentations try - it can also work as a good mindmapping tool.
posted by coffee_monster at 10:24 AM on March 10, 2010

Second Papers. If you are doing any biochem-related stuff, I've got more suggestions (ImageJ, MacPyMol, etc., along with non-free programs like MacVector.) I use Kaleidagraph, but there are probably other programs out there - it's nice to have something other than Excel to use for data analysis and graphs. Note that Kaleidagraph is - like ChemDraw and other expensive science software - the sort of thing you want your advisor to pay for. Papers is cheap enough with a student discount that I didn't bother.
posted by ubersturm at 10:47 AM on March 10, 2010

Zotero + FreeMind.
posted by turkeyphant at 11:07 AM on March 10, 2010

For storing and organizing jottings, I use KeepNote. It's very simple - basically just a rich text editor with Outlook-style folders/message hierarchy - which to me is a strength. I use it for just about everything.
posted by PercussivePaul at 11:10 AM on March 10, 2010

Also! If you know how to prepare a good figure with consistent style, you'll save yourself a huge amount of hassle come thesis time. Every PI has their own preference, so you should learn theirs, but I've found gnuplot, Origin, Igor Pro and Adobe CS all to be of use and ten zillion times better than Excel.

Seriously. Please don't ever use Excel unless there's a gun to your head.
posted by beepbeepboopboop at 11:53 AM on March 10, 2010

EndNote and Papers are pretty standard for Mac users in the sciences. EndNote will ingratiate you with PIs who are writing papers and proposals.
posted by Blazecock Pileon at 12:01 PM on March 10, 2010

I use endnote and am not in the sciences.. it's a godsend for citations and notekeeping -- you just have to make sure that your citation format is available, or you have to make your own which is annoying (I had to do the latter -- totally worth it, but very fiddly).
posted by modernnomad at 12:28 PM on March 10, 2010

There are a lot of cool web-based science thingies out there. Which is cool if you always have web access. People usually have access most of the time these days, but most of the time is NOT all the time.

I use EndNote for three reasons:
1) Historical. All my old papers were written using EndNote, so my research library is organized by EndNote ref number. I don't want to have to re-enter all of that, reorganize things, and learn a new interface. (I print out papers, slap the EndNote ref # in the top corner, and file them by number. PDFs are saved attached to the reference itself within my library.) Whichever program you intend to use, realize that you are likely going to be stuck with it for a long, long time. If you don't like it immediately, try something else before you commit.

2) Access. EndNote has a web option but is pretty firmly committed to ensuring that your references are stored on your computer (according to the EndNote reps I have spoken with). If the network goes down (which it occasionally does) I can still work. If I am on a plane, I can work. If I am lost in the woods trying not to get eaten by bears, I can work as long as my laptop battery lasts (or until the bears catch me). I do regular backups of my library, both at home and at work, to make sure I don't lose anything due to drive failure. Aside from PDFs my entire library could easily be stored on a USB drive and taken anywhere I go, meaning I can work on any computer with EndNote installed if it comes down to it.

3) Collaboration. EndNote is pretty standard. Most science people I know use it, and have done so for some time (including my grad school adviser, my current mentor, my committee members, labmates, etc.). I can share documents with any of them and all of us can edit things. The "traveling library" option allows me to include references with a document, and any of us can edit them and send back to the group. EndNote works with Word, Pages, OpenOffice, etc. these days, to varying degrees. EndNote is available on Windows or OSX, and libraries can be moved between platforms with no problems. As long as you keep references unformatted, you can share files with no worries, without having to convince your PI or colleagues to learn a new program just to work with you.

A fourth reason - site licensing - might apply to you at your institution (it does not apply at mine). A great tool that you have to pay for out-of-pocket might not be as nice as a good tool you can legally obtain for free. Bear this in mind when making decisions.

Other people I know use Evernote and Papers and they are pretty happy with them; I haven't played around with them much myself. My worry is cross-platform. I don't necessarily like using something that will disappear from my list of options if my operating system changes. The vast majority of programs I use on my Mac now are the same ones I used on Windows computers while in grad school. I wouldn't use this as a reason NOT to get excited about a Mac-only program, if it fits your needs, but be prepared to look for alternatives if you some day end up working for a government research department that forces you to use Windows. Like the one I work for now. (Sigh.)
posted by caution live frogs at 12:40 PM on March 10, 2010 [2 favorites]

Sente really can't be beat. It combines the best aspects of Papers and EndNote, and will also pull down articles from the web based on your interests. I honestly can't sing its praises enough.

You can try it for free for 30 days. Give it a shot. It's honestly the best academic reference management software I've ever seen.
posted by solipsophistocracy at 12:52 PM on March 10, 2010

Oh, also, w/rt caution live frogs' comment, you can export most if not all of your data to a format that EndNote can read in case you're collaborating with others who prefer that software.

Also, web access enhances Sente, but is totally unnecessary for most of its features. The fact that I can assign a tag to any paper, then write in Word, citing the paper w/ {whatever tag I chose}, and then drop the file into Sente to have it format the paper in any one of a dozen different reference formats is unmitigatedly awesome.
posted by solipsophistocracy at 12:55 PM on March 10, 2010

Most important info: find out what packages your PI uses and use ideally the identical ones, or at very least ones that share data well with him/her. Anything else is just asking for trouble.


If you're starting gradschool in chemistry and you;re at all organic chemistry or bio-organic chemistry based, you should have a copy of ChemDraw.

Your university should have either a site license to download for free, or at least have a discounted package.

I use endonote, and a lot of other academics do to. Your newschool/web-based app may be better, but you're fighting inertia.

To get citations entered correctly into your database, you should download them from searches from Web of Science or Scopus (again, your insititution should have access) : manual citation entry is for chumps. Get good at really using these and other databases to read around your field...... Remember: 6 months in the lab saves a day in the library!
posted by lalochezia at 3:06 PM on March 10, 2010

DevonThink. For an awesome combo, splurge for the Pro Office version + Fujitsu ScanSnap scanner.
posted by webhund at 4:13 PM on March 10, 2010

Your newschool/web-based app may be better, but you're fighting inertia.

I used EndNote for several years, and it sucks comparatively. If you can get software that is superior in nearly every way but still willing to play nice with the dated "inertia" laden programs, why wouldn't you?

Sente, man. Sente. It is unstoppably awesome.
posted by solipsophistocracy at 4:29 AM on March 11, 2010

VoodooPad is worth a look at least. It's more of a personal wiki with extra bells.

For brainstorming, you already have FreeMind above (look for the Intel native 0.9.0RC7 release instead of the PPC 08X series). There is also MindMeister and XMind, both available in a free form.
posted by chairface at 9:01 PM on March 13, 2010

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