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Why Linux is awesome

Before you rush to the comments and express your opinion about this title, let me make something clear. I do not expect anybody to erase their operating system and install Linux after reading this post. Actually, I do not care whether you use Linux or another operating system. All I want is to share what I have learned by using Linux, and why it made me a better scientist.

The mouse that infects your brain

About a year after I started to use Linux, I was surprised to realize how uncomfortable working on Mac and Windows had become. I could not quite pinpoint the problem, but I had the vague feeling that something was missing. Yet everything seemed to be there. When I could finally formulate it, I realized that what was bugging me was the discomfort that all the possible options had been preconceived for me. I could click on option A, I could click on option B, and if I liked neither of those, there was no option C.

But most surprising was that I had never realized this before, because I had no idea of all the things you can do with your computer. I...






Nature on code sharing

A recent Nature editorial entitled “Code share” discusses an update in Nature’s policy regarding the use of software. Interestingly, the subtitle is

Papers in Nature journals should make computer code accessible where possible.

Yes, finally! The last decade was a transition period, which, in the history of bioinformatics will probably be known as the “bioinformatics revolution”. Following the completion of the first genome projects, the demand for bioinformatics rose steadily, to the detriment of biochemistry and genetics, which have now fallen from grace. Something as traumatic cannot happen in a day, and it cannot happen without pain. Actually, the transition is still ongoing and this regularly causes difficulties of all kinds in biology.

One of the most perverse effects of the massive popularization of bioinformatics is that senior scientists were not properly trained for it. This led to an implicit view that bioinformatics is a tool, somewhat like a microscope or a FACS. This explains why the materials and methods section of the first papers using bioinformatics was often reduced to something like “all the bioinformatics analysis were performed using R”. In other words, “we got some bioinformatics software and asked a qualified technician to use it...






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