Bioinformatics tools for the rest of us


To all Mac OS X users: a whole pile of bioinformatics tools have been made freely available to us, as announced on

Many Life Science researchers need bioinformatics tools for the desktop. But many of the common Open Source tools are difficult to install for people without much Linux/Unix knowledge. We have created a user friendly install package for the MacOSX platform. The package installs most of the common bioinformatics packages: EMBOSS, Blast, HMM etc and also installs some biological databases. Together with the packages it is possible to configure webservices e.g. Blast. Researchers will find it very useful to be able to install a user friendly GUI in top of EMBOSS (embossRUNNER).
All packages can be downloaded at Detailed instructions and HOW-TOs have being published on the latest issues of EMBnetNews (free from

It's a 252MB gzipped file that will take up about 850MB installed. You'll also need to install X11 for Mac OS X; this is included on the Panther CDs (disc 3), but isn't installed by default. You'll need a fast connection and a bit of room on your hard disk for all this stuff! They also recommend that you get a three-button mouse, the one thing I'm lacking on my laptop.

The instructions for installation are in multiple volumes of EMBnetNews, and unfortunately they've been superceded in steps. Volume 9.1 has the original, rather convoluted instructions, but you might want to see them to get the list of stuff that is going to get plopped onto your computer. Volume 9.2 has details on Blast and GUI frontends. Volume 9.3 has more on Blast and performance information, and describes a major change in the installation procedure: it now just takes one double-click on a single installer package to put everything in one directory on your computer (in other words, ignore the instructions in 9.1). Volume 10.1 is just a short note listing some recent additions.

This probably isn't something anyone should do on a whim. It's going to require about as much horsepower and resources as, say, the latest version of Diablo, or whatever the hot new graphics-intensive video game might be. And once you've got it running, it's not going to be obvious how to do anything with it unless you've got a bit of molecular biology background.

I've put it on my machine, and it was fairly straightforward; it only took about an hour for everything, and that includes the download time (I have a fast connection). Don't ask me for help with it, though, I'm just tinkering myself and puzzling my way through all the bits and pieces.


Are these more advanced than what’s available for us Mac-o-phobes? And (again for us Mac-o-phobes) what are some good bio-info resources beyond NCBI?

Of course they are more advanced, by definition: they run on a Mac.

Seriously, though, the guts of the software are no more advanced than what you can run under Linux. They’ve just been ported to OS X with ways to easily install them for us Mac-o-philes.

I’ve been playing around with installing perl and bioperl on Windows XP. Perl is a scripting language that is particularly good with text data, e.g. webpages and sequences. Bioperl is a huge set of modules giving bioinformatics applications to perl. This stuff is useful if you want to do more than use the clunky web interfaces for bioinformatics tools, which become onerous with any amount of repition.

I’ve begun posting some notes on EvoWiki, installation is painful the first time, not nearly so bad once you figure out what they heck you’re doing. Watch the page for more…

I use perl to manipulate the input and output for a couple of programs I have chained together to study weighted parsimony.

Though a pc user who isn’t all that interested in switching to Mac, despite a sweet OS, I saw the 23” cinema desplays today at CompUSA. drool…drool…

For a three-button mouse on a Mac laptop, try SideTrack. It allows (among other things) a tap in the trackpad’s corner to act as a second- or third-button click.

And now there is the *30 inch*:

Hey, it is just money!

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This page contains a single entry by PZ Myers published on July 5, 2004 2:00 PM.

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