The recent popularity of the article A Farewell To Bioinformatics has led me to debate what many of my pure computer science friends see as big problems in bioinformatics—poor code quality, lack of testing and documentation, and unreliability. I said that things generally seem to be getting better over time, but they said they keep hearing about vague "improvement" in bioinformatics with no concrete examples.
As just an undergrad (in CS and Molecular Biology) with a short history in the field, I couldn't come up with much to say. So I turn to you.
Can you give any specific examples of how bioinformatics has improved over time? From specific tools and file formats to general practices?
Thanks for your time!