I’ve seen a lot of imaging software packaged for the Debian Linux distribution, so I decided to set up a machine to try it out. Debian is a popular choice for scientific software, known for its stability and the massive library of pre-built packages available for easy installation through its package management system.
Neuro Debian is a six year old project to make high quality software readily available to researchers everywhere (a full description is found in this recent publication by the principal authors). It places strong emphasis on the correctness and interoperability of the software packages, resulting in applications that install automatically and produce reproducible results. In practice, it’s employed as a supplementary repository for specialist software packages, that integrates completely into Debian’s existing package manager. There’s the promise of entire compatible software systems to be installed in a few clicks. Let’s see how it fares.
Downloading Debian was straightforward. There are a variety of installation techniques – live network installation, DVD and CD images to download and burn, torrents, and live test images to try the OS from a disc or stick. I made up a Parallels partition on my Mac for the new virtual machine, giving it 2 GB RAM and 2 cores, and installed directly from the minimal 440 MB image I’d downloaded. Been a while since I saw an installation that small, but I’m sure the packages will be much larger. I enjoyed the old-timey non GUI installation screen, once upon a time we called this a ‘user interface’, now it’s coming back into fashion like an 8-bit video game.
It’s also been a while since I saw an OS start and stop as quickly as a stripped-down Debian installation. We get so used to Mac OS and Windows loading…and loading…all sorts of essential something. Debian gets to the point, and does it in a few seconds.
I installed both and had to hunt through the menus to find them filed under ‘Graphics’, which is fair enough, I suppose. Some of the other programs I later installed made it on to the ‘Science’ menu.
The other category I was particularly interested in was Imaging Development, and as you may expect it’s pretty technical. Lots here for the software developer. Exploring the other categories is left as an exercise for the reader (it’s not called “I Do Psychophysics”).
Installed software has a short summary in the package manager. Running the programs again reminded me of just how quick computers can be when you strip away the extraneous extras. The applications jumped onto the screen and were ready within a second. This particularly reinforced the advantage of having a dedicated system – even one running as a virtual machine, as here – over running imaging software on your regular desktop computer. Fewer distractions, too.
Overall, I was highly impressed. A new user could download and install an entire operating system, plus imaging applications, and be up and working within half an hour. Some experience with Linux software is of course useful, and some of these applications would also benefit from some command line experience. But since the software is downloaded and installed as binary executables, with all dependencies handled, there’s no chance of it not compiling correctly. Neuro Debian bills itself as the “Ultimate platform for neuroscience” and I think they have a case. Great packages that install themselves and work out of the box: this is free software done right.