My PhD using only free and open source software

Tux the penguin, mascot of Linux

I have been advocating in favour of free and/or open source software ever since I started using GNU/Linux in 2005 during my second year of undergraduate. I am not entirely against paid or proprietary software till they are legitimate and not a boot leg copy (however, I do have security related concern on using proprietary software). I have learned computer through out my childhood using bootleg copies of software. It was not my mistake I was 15 when I got my first Pentium I computer which came with Windows 95 pre-installed however, that installation was a cracked copy provided by my dealer. As a teenager I was only happy that I have a computer rather than bothering about whether its legitimate or not. However, when I learned more about piracy issues and security related to the cracked copy of software I got rid of all the cracked software and installed Fedora core 5 on my second computer and since then I am using some variant of GNU/Linux on my computers. Only my current laptop has a dual boot with Windows 7 because it came pre install (legitimate this time 🙂 ) and I will loose tech support from the company if I get rid of it (I think this is really cruel why can’t I get support on my hardware if I am not using Windows). I have been using free and open source software for a while but I always had this thought in my mind whether they are good enough to do whatever I want to do for example will they be good enough 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 few months. I am a computational biologist and my research is all about computing biological phenomenon, which involves a variety of software. Through out 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 British Journal of Cancer during my PhD and all the work done by me on those two project were using free software. So when current free and open source software are good enough for a doctoral research then I believe that they are more than enough for an average computer user. Which means in most of the computer usage today we do not need any proprietary software. By using free and open source software 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 free and/or open source software 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 suit 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 meta data 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. Its one of most successful alternative to Adobe Illustrator.
Gimp: a cross platform free and open source software for image editing. Its one of most successful alternative 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). Its 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 SVG format which can be easily edited using Inkscape.
Avogadro: a free cross platform molecular editor. A part from structural editing it can perform semi empirical quantum calculations using MOPAC. Its 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: 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 its good for you then its great but do not encourage the use of pirated software instead use a free alternative.

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