Open-source in academia and research charities

I discovered GNU/Linux in 2005, by attempting to install Ubuntu in a dual-boot with Windows XP. Windows got wiped out in the process and I was left with Ubuntu. This was kind of a fortunate mistake, because I never looked back. Since then, the only OS running on my personal computer is based on GNU/Linux and it is highly unlikely that I will ever go back to MS OSes. And since then, I’ve been puzzled by the dominance of proprietary softwares in laboratories.
The GNU/Linux ecosystem offers a handful of applications that can be used –or are used in some cases– in laboratories. This is mostly the case in specialised applications used for example to solve protein structures, or to do powerful statistics. In fact, there even is GNU/Linux distributions out there dedicated to the biological sciences or nuclear physics. These two distributions offer a handful of tools pre-installed and you normally do not need to install anything else. Or if you do, the software “package” is just one click away, a time-saving system when you consider that on Mac OS X or Windows you need to browse the internet, download the package and then install it.


GNU/Linux systems are nowadays widespread in structural biology laboratories, some companies or laboratories make the ability to use GNU/Linux systems a desirable or an essential skill when they look to appoint someone. And yet, most academia labs I’ve visited run on proprietary OSes. GNU/Linux systems have the reputation to be complicated to administer, with a lot of tinkering in configuration files or the requirement to use the command line. While these systems do offer a lot more possibility to the savvy user and the command line being not so complicated after all, and far more faster than clicking your way through the desktop, they are by no means too complicated for a non-technical user. All you need is the will to change your habits. When I installed Ubuntu, I couldn’t consider myself a geek and I certainly had not much knowledge about computers. I did have a shot at programming with AMOS Basic on an Amiga 500 when I was a teenager (I still have fond memories of this machine), and I did know about DOS. But this was long buried under a more or less consumerist approach to computing. In 2005, Ubuntu was a bit rough around the edges, and I did have to tinker to install a proper driver for my graphic card, or to get the WiFi card running. But I managed, thanks to the very extensive documentation available online and the community forums. Nowadays, I only tweak my computer when I want to. Either to test a new distribution or bleeding edge softwares. Furthermore, there is no reason not to run a GNU/Linux based system: you want novelty in desktop concepts ? Gnome 3 or Unity are using a new paradigm in desktop environment (DE) and layout since one year; and if you don’t like this paradigm, you can always install an another DE (all the DEs in this gallery are open-source). In fact, both Mountain Lion or Windows 8 are copying ideas from the open-source community. You think that the 3D effects in Windows 8 or Mac OS X are cool ? They exist in Linux since 2006. Microsoft is copying Apple’s app store ? No, they are both copying the concept of repositories and package managers that are the very foundation of any GNU/Linux systems –since their beginnings in 1991.
The reason why I am puzzled by this low profile of GNU/Linux systems in Academia is that, you would think that people in this community would be more interesting in the technical solutions out there. I worked in a charity where the software we used was imposed: I had to use Microsoft Office instead of Libreoffice, Endnote instead of Zotero, Photoshop instead of The Gimp, Adobe Illustrator instead of Inkscape,Canvas instead of Scribus. It seemed to me that there was a lot of money put into licences that could have been spent in hiring more people or funding more research. Worse still, the IT crowd decided that their servers would run under Windows. When one considers the security issues faced by Windows, it seems a bad idea to a server version of it. At the very least, a debian-based server would have been more secure.It seems to me that the big problem with the adoption of open-source operating systems isn’t born on their difficulty. This was true, but this isn’t anymore. Nowadays, when you go to PC World (in the UK), FNAC (in France, Spain and Portugal) Mediamarkt (Germany, Spain and Portugal) or Saturn (Germany), you will have hard time finding a PC without an operating system. The problem is that you are not buying only the computer, with a free Windows on it. You are actually buying the computer and the operating system, the latter is discounted, but you are still buying it (or rent it, given the type of the licence). Most people don’t know about this and they often think that Windows comes for free and no salesman will ever explain them that they have to pay for that. This is a case of tying that flies in the face of consumers’ rights: not only do they not know that they are paying for a product, if they know about it, they will have hard time getting Windows removed from their computer without losing the guarantee (this depends on the manufacturer) and get refunded. And this is illegal, at least in France, where Acer has been forced to reimburse someone for unwanted MS “racketwares” (fr).Another problem is the widespread, and unjustifiable, use of proprietary formats such as .doc or .docx in human resources or by scientific journals. Try to apply to a position by sending your CV as a .odt, or to publish in a journal by sending the manuscript in the same format. This won’t work, they won’t accept it on the grounds that they “cannot read it”. This isn’t true, though, as the latests MS Office suite© is able to read .odt files. Better still, open-source softwares such as Libreoffice or Abiword can be installed –for free– to read it. Not to mention the widespread use of MS Office© by the academic staff, which forces the students to buy (or acquire illegaly) a licence for this software. Again, there is no justification for that. I know that some administrations have turn to GNU/Linux or open-source softwares for their operations. This is the case for the French Assemblée Nationale, why couldn’t it be the case for universities, charities and even scientific journals?

In any case, while I might have some understanding for someone buying a computer as they would buy any other appliance, I still have problems to understand why IT services in universities or research charities waste millions of pounds on proprietary OSes and insecure servers while there are professional, free alternatives out there. Even more so nowadays that we are facing financial hardships translating in reduction of fundings or donations.

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About ravingscientist01

Trained as a molecular geneticist, I did a PhD in biochemistry and molecular biology. I am interested in science, its communication, the impact it can have on policies as well as the impact of various policies related to science may have on the latter.
This entry was posted in Computing, Linux, Policy, Science. Bookmark the permalink.

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