An Apple a Day Keeps my Research Advisor Away
January 29, 2008 9:27 AM   Subscribe

New Macintosh user needs help getting his Pro set up for academic research.

My labgroup ordered a pallet of apples and I have been on a windows box until now. I was hoping you guys could tell me what software I need and what procedures I'll need to do in order to get back up and functioning. My main needs are: tunneling into a unix server and running remote programs via an x window (you can tell how much I already know about that.), pdf organization (I've got endnote, but I hear I can search in a group pdfs from the finder), and how to utilize all these fresh cores as an xgrid server (it's already set up by a coworker I believe, but I'd to know how to code my own too). Any other suggestions more seasoned scientists might have would be appreciate too. Thanks!
posted by Large Marge to Education (10 answers total) 9 users marked this as a favorite
X11 should either be installed or on the installation disc. Then immediately upgrade it. SSH is installed by default.
PDF organisation - Spotlight will search pdfs for you. I personally keep stuff filed online at CiteULike. Check out Skim for annotating pdfs.

XGrid is easy enough to use - you just write a shell script wrapper.

What research field are you in? I've a fair few links for physical scientists using Macs (thanks to running my own site on my own research area), and there's which is fairly general.
posted by edd at 9:40 AM on January 29, 2008

Oh, that XGrid link has changed a bit. This might be more useful. (And you probably want to install the Developer Tools, downloadable off or probably on an installation disc too)
posted by edd at 9:45 AM on January 29, 2008

Best answer: Regarding PDFs: there are a number of cool Mac apps for scientists. Take a look at Skim ( - it is much faster than Acrobat, and lets you take notes or look at a figure in its own window next to the appropriate text. Many people use Yojimbo ( for PDF organization, although I am looking at Papers ( as a way to organize and read PDFs. It is made specifically for scientists.

You'll still need Endnote to cite in Scientific papers (I think), but it is a kludgey mess to use on a day to day basis. I think you'll enjoy these other apps much more.
posted by SciGuy at 9:47 AM on January 29, 2008

Skim is great. It integrates nicely with BibDesk if you use LaTeX (though it sounds like you don't since you use EndNote).
posted by zsazsa at 10:20 AM on January 29, 2008

Papers is pretty good for managing paper PDFs. It doesn't integrate with word for citation, though, so while it maintains a great local database, I don't think it replaces EndNote yet. I've also had major trouble getting a good workflow going between Papers and EndNote — export to EndNote always kind of screws up the entries, like getting them all to show up as "Bill" instead of "Conference Paper" or whatever. Papers is also not great at managing anything other than papers. You have to kind of kludge books or websites or whatever into it. Still, it's worth a look.
posted by heresiarch at 10:37 AM on January 29, 2008

Response by poster: indeed I am in the physical sciences. App phys.
posted by Large Marge at 11:10 AM on January 29, 2008

I use Zotero to manage all my pdf's, books, articles, webpages and other references; once you try it, you can adios to endnote.
posted by ddaavviidd at 11:13 AM on January 29, 2008

you can say adios - and I forgot to mention it's free!
posted by ddaavviidd at 11:27 AM on January 29, 2008

Papers is really solid. I use it all the time and highly recommend it. I also do occasional web development and need to check out my work in internet explorer... so I installed parallels and a virtual xp machine, in which I run MultipleIE, which installs every version of internet explorer and makes them play nice with eachother.
posted by macowell at 1:19 PM on January 29, 2008

In that case you might want to visit the OS X HPC page and Hitoshi Murayama's Mac OS X for Physicists page (although that's not seen an update in a while so there's no stuff dealing with Leopard there that I can see, and some bits are out of date as a result). Mine has a fair chunk of astronomy specific stuff but some more general purpose bits too. Apple has a list of software too.
posted by edd at 3:37 AM on January 30, 2008

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