Are you using a Mac as a main computer for bioinformatic work?
I use a few Macs for script and software development. I use the lab's Linux cluster for launching larger analyses.
What positive points do you see about using a mac for bioinformatics?
Unlike most handbuilt Linux desktop options, the hardware and software work well together, so I don't constantly need to be a sys admin like I did with Linux. Wireless networking just works. Plugging in a laptop to do presentations just works. Power management settings just work. The OS X operating system is less fragile to kernel and hardware changes and is easier to fix on my own, when such rare problems arise. OS X can run useful (if still commercial) visualization and productivity tools with easy access to a UNIX terminal, which Linux still cannot do (generally speaking). Many native GUI and command-line tools are available for doing source code control on OS X, so I don't lose any abilities there.
What negative points do you see about using a mac for bioinformatics?
A lot of open source gets distributed as RPM packages or similar, while package systems for OS X are a bit less friendly, in that regard. Some open source GUI apps are X11 based, which not only makes them look ugly but introduces a whole separate set of key shortcuts to learn, just for Linux-y apps. This also makes integration difficult — copying and pasting between native OS X apps is a nice feature, but is difficult between native apps and X11-ized apps.
If you're running a computational cluster, then Linux is a winner here, for the simple fact that the stripped-down hardware you need for that application is cheaper per node. You don't need a Mac Pro's super-duper graphics adapters, for instance, unless you are running custom analyses on fancy GPUs.
On the other hand, now that Thunderbolt shows up as an Ethernet adapter in Mavericks, I'd be interested to see if it gets used as a very fast interconnect for cluster work (a cheaper alternative to Infiniband, for instance).
Ease of installing software (talking about bioinfo software here)?
Depends on the software. Most of it can be compiled easily but you'll need to install Xcode, at a minimum, which used to be a PITA to download (used to need an Apple Developer Center account and navigate Apple's ADC site maze) but it is now pretty easy (OS X App Store + Apple ID + one or two clicks). Just about everything else that you can't compile on your own is something you can manage with macports or homebrew.
On the subject of macports and homebrew, pick one or the other, not both. They will step on each others toes as far as managing dependencies. I prefer macports, but I suspect it is largely a matter of how much you like (or dislike) Ruby, if you want to try homebrew.
Freedom to hack quick solutions for custom problems?
Decently modern versions of Ruby, Python, Perl etc. come pre-installed. So long as your sys admin has given your account admin rights on your Mac, you can compile and install whatever else you need through Apple's Xcode/clang, GNU's gcc and macports or homebrew.
Whatever opinion you want to share about this question
As a political matter, I love Linux's openness and customizability, but as a daily-use operating system, its interface just isn't very well engineered (just one person's opinion) and I suspect that no amount of catch-up work to imitate commercial operating systems will make that aspect of it as easy and reliable to use as OS X. Tools which other staff use for writing and managing papers (Word, Endnote, etc.) just aren't available, and open source and online "equivalents" do not quite make the grade, IMO. Managing document citations in a shared Google Doc is simply a non-starter, for instance. Of course, I'm less amenable to making compromises because I'm a pretty lazy human being. If your time is free and you love the OSS movement and you're willing to put in the work, you can do a lot of these things in Linux.
Why should I (or not) think of getting Macs for our lab?
I suspect it will reduce your administration costs, at the up-front expense of slightly more expensive hardware and the cost of commercial software. You'd need to balance that against the productivity gains from having your staff be able to collaborate together and share data more effectively. Compared with Linux, this is probably a plus mark in favor of OS X and Windows, generally speaking. On the other hand, you're going to spend a bit more up front. Six of one, half dozen of another. You'll need to decide what your priorities are with this investment, I suspect.
I think some people are confused about what you want an answer for.
Are you asking whether or not Macs are a good buy for "middle tier" workstations that users will have on their desktops? Or are you asking if a mac is a good choice for a (single) compute server that will service the needs of the people in your lab when they don't want (can't) get access to a larger (presumably linux) compute cluster?
I think you are asking for recommendations on the latter, but it seems like some answers are addressing the former.
Hi Steve, the question could have been more precise and I added an EDIT portion to clarify regarding your comment. At the moment of writing the question, I was considering one or two computers that would fill these needs 1) it would be used by lab members so that they are more independent in their analyses 2) I would use that computer daily for my work.
One thing which I don't think anyone has commented on yet is the higher cost of a Mac and future OSX updates. Would you want to exchange the costs of more compute power for a more slick environment?
For what it's worth, it looks as if future OSX updates will be free just since the new OS (10.9) is a free update from many previous versions (I believe as far back as 10.6). That having been said, in recent years, upgrades have only cost ~ $20, which is not onerous by any stretch of the imagination.
See my reply to Steve's comment. In case 1, maybe I would consider a slicker environment for the many potential users (most of which have Mac laptops). For case 2, where I am the sole user, I would have a tendency to go for a more powerful penguin rather than a comparatively weaker apple for the same price.
If it is a multi-user system the interface shouldn't matter. It is probably best to set it up so that users remote connect to their accounts and run jobs in the same way they would a server or computer cluster, but probably without the job scheduler. Although that may be a good idea just for management depending on the number of users. Otherwise they should be trained in making sure there are no other big analyses running that theirs would interfere with, to talk to other lab members before running jobs that will run for a very long time, etc.