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...