My PhD using only free and open source software

I have been advocating in favour of free and/or open source software (FOSS) ever since I started using GNU/Linux in 2005 during my second year of undergraduate. I am not entirely against paid or proprietary software as long as they are installed using a legitimate and not a bootleg copy. Throughout my childhood, I have learned how to use a computer using only bootleg copies of software. It was not my mistake I was 15 (1999) when I got my first Pentium I computer that came with Windows 95 pre-installed from a bootleg copy done by my computer dealer. As a teenager, I was happy that I have a personal computer than bothering about whether it is legitimate or not. However, as soon as I learned more about piracy issues and security related to bootleg copies of software I got rid of all of them and installed Fedora core 5 and since then I am using one or the other variant of GNU/Linux distribution. Even though I was pretty convinced that FOSS is good I wasn’t sure enough that they will be useful for my engineering studies or when I will do PhD.

Now I am in the final year of my PhD and hopefully will finish in a few months. I am a computational biologist and my research is all about computing biological phenomenon, which involves a variety of software. Throughout my PhD in the past three years, I have not used a single paid or proprietary software, all my research was done by using free and/or open source software and the results came out really well. I co-authored two papers published in Nature Chem Biology and the British Journal of Cancer and all the work involved in those publications were carried out using only FOSS. So I wonder when current FOSS is good enough for a doctoral research then they are definitely enough for an average computer user. That implies most of our computer usage today we do not need any proprietary software. By using FOSS we are not only giving ourselves more options to choose from but also it refrain us from using pirated software, which is a crime.

Here I have given a list of FOSS which I used during my PhD for both scientific research as well as general computing.

For general computing

For scientific computing

With my successful experience in using free and open source software in my research as well as in my everyday computing, I urge all my friends to give a try to GNU/Linux and the open source software which comes along with it. Even if you are using Windows you can still use many of the cross-platform open source software. If you can buy a proprietary software and you think it is good for you then its great but do not encourage the use of pirated software.