Corycia

Several people have been asking me about what useful applications there are on OSX for academic scientists, so I thought I’d write a short post summarising them. Hopefully this will give people a head start in doing science and scientific computing on their Macs. Not all the programs list are free, but they are all good I think!

Caffeine (free): A very handy menubar program that lets you control whether your Mac goes to sleep or not. Just click the icon and your Mac will stay awake during your simulations.

Canary (free): There are zillions of Twitter clients. This one is free and works.

Cyberduck (free): If you’re moving your simulation files around, you’ll need an FTP/SFTP client. Cyberduck is free and good, and is easy to use.

DiffMerge (free): Lets you compare files and folders for differences and merge if desired.

Evernote (free-ish): I use this application more or less daily for note-taking. I have a terrible memory, so I jot down notes at meetings as an alternative to using a notebook or lots of scraps of paper. Think of it as being a electronic lab book. As well as text, you can also record images, photos etc., and everything is synchronised to an online server meaning you can also access your notes if you’re away from your computer. Text in images is OCRed, and everything is searchable – which you can’t do in a lab book! There is a paid service, but I’ve not needed it yet.

GeekTool (free): Lets you display any Unix command on your desktop. For example, you can have ‘top’ running continuously, letting you know at a glance how your simulations are running.

iStat Menus (free): A handy menu bar panel that tells you what’s happening in your Mac; CPU, temperatures, network activity, memory and disk.

LockTight (free): Gives you a handy keyboard combo to lock your desktop before you walk away from it. Handy in shared offices.

MacGPG (free): Gives you transparent encryption for your files and email. You’ll also want GPGMail.

MacTeX (free): You’ll need a decent TeX editor when writing papers. Personally, I just want something that works on all files and sub-formats, and installs without any fuss. I don’t care about messing around with funny customisations. MacTeX just installs, and works. The front-end that gets provided is TeXShop, which isn’t as good as the WinEdt you can get on Windows, but is fine.

Mathematica (paid): Mathematica is expensive, but is so powerful and useful that it’s worth the money. If you use it you already know how good it is. If you don’t, take the time to try it out and you will probably get hooked.

Matlab (paid): Not as good as Mathematica in my opinion (although it’s faster for lots of numerical stuff), but it’s used so widely that you willwant to be able to open and edit code from other people.

Microsoft Office (paid): Yes, I know about OpenOffice, and it’s ok, but honestly it’s simpler to just buy a copy of MS Office. However, Keynote makes better-looking presentations.

Merlin (paid): MS Office on Mac doesn’t have MS Project. If you need to make project plans and Gantt charts, then Merlin is probably the best program. It isn’t free though, and there are free alternatives. OpenProj is probably the best free one.

Papers (from Mekentosj): This is a wonderful, wonderful application for keeping track of research papers, both your own and the ones you read and cite. It connects to most of the databases, automatically generates BibTeX citations (very handy!), and lets you keep collections of papers for the various projects you are working on. It’s pretty reasonably priced too. I also use it to keep track of things like manuals, presentations, guides etc. Its only downside is that it’s aimed at PDF documents only. However, it’s a much better way to keep track of all the papers you look at than the often-used method of lots of little folders all over your computer.

Plaxo (free-ish): Plaxo is a really simple service to synchronise your calendars and contacts with the online world. Basically, it connects all your email accounts together. On Mac there is a little application that sits around synchronising your Mail and iCal, and again you can view everything on the web. There is a paid service which gives more functionality, like automatically removing duplicate information.

Enthought Python Distribution (free for academics): Python is a great language for tying together other simulations. The Enthought distribution provides all the scientific packages you might want like NumPy, SciPy etc. in one easy installer. Brilliant. The distribution also includes matplotlib, which make data visualisation easy.

Sapiens (shareware): Application launchers are a personal thing, but for fans of the Macbook trackpad, Sapiens (by Donelleschi) is brilliant. You’ll probably get rid of your Dock before long.

Skype (free): You’ll almost certainly already have this! It’s pretty much essential for talking to people overseas.

Smultron (free): You’ll always have a need for a decent programmer’s text editor. My personal choice is Smultron. Bizarrely for something used so often by people, there isn’t really a great editor. Smultron is the best free editor I think, with syntax highlighting etc.

Sticky Windows (shareware): Another great little app from Donelleschi. I can’t get on with Spaces, and whilst Expose is ok, it’s sometimes nice to move your open windows out of the way. Sticky Windows lets you do that, leaving little tabs at the side of the screen. Great stuff.

VMWare (paid)/Virtualbox (free): Sometimes you have to run codes that aren’t Mac-friendly. The easiest way to do this (although a bit slower) is to use a virtual machine. In my opinion, you should either use VMWare (which costs a small amount), or Sun Virtualbox, which is free.