My PhD using only free and open source softwarePhD ·
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
- Libre/Open office: a cross-platform free and open source office suite for word-processing, presentations, spreadsheets etc. I used Libre office to write my lab book, short reports, applications and resume.
- Mendeley: a cross-platform reference manager. Its a really cool software to manage the references similar to EndNote. But it has the advantage that it can manage the PDFs and can also fetch the metadata straight from the PDF files. I also use it to sync my reference library as the BibTex library which I can pull straight into my LaTex document.
- TexStudio: a cross-platform free and open source LaTex editor for writing my PhD thesis. It definitely makes writing LaTex document so much easier.
- Inkscape: a cross-platform free and open source software for creating high-quality vector graphics. It’s one of the most successful alternatives to Adobe Illustrator.
- Gimp: a cross-platform free and open source software for image editing. Its one of the most successful alternatives to Adobe Photoshop
- Thunderbird: free email application to manage my university emails more efficiently. An alternative to the Microsoft Outlook.
- Artha: an open thesaurus project with features like global hotkey (Ctrl+Alt+W). It’s very similar to the WordWeb and very useful.
For scientific computing
- Modeller: a cross-platform free program for academic research for homology modelling.
- PyMol, VMD and Chimera: cross-platform free programs for molecular structure visualization and editing.
- Marvin Sketch: a cross-platform free program for chemical structure drawing. A cool feature about this program is that it can export the drawing into an SVG format which can be easily edited using Inkscape.
- Avogadro: a free cross-platform molecular editor. Apart from structural editing, it can perform semi-empirical quantum calculations using MOPAC. It is also very useful for generating input files for software like Gaussian and GAMESS.
- Gromacs: a free open source molecular dynamics engine. It supports several different force fields, some are already included in the source code some can easily be ported. Its very fast and can easily be installed on large computer clusters.
- Autodock: a free software for small molecule docking.
- HADDOCK: a free web server for protein-protein docking.
- Padre: a free and powerful editor for writing Perl scripts.
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.