I have opened a new discussion on Biostar, on ‘What is the best question that you have asked, or heard asking, in a bioinformatics seminar?‘
For a scientist, it is very important to be able to make good questions; seminars are a good place to practice. In my case, I am lucky because in the building where I am doing my PhD there are always a lot of seminars, and at least one each week is about bioinformatics.
My favorite question is to ask about the controls that a bioinformatician used to test the software he wrote, or the analysis he did. When I was studying in Bologna, my former professor of Molecular Biology used to repeat us, in almost each lesson, that the most difficult part in designing an experiment is to choose the best controls. I believe that the choice of controls is the moment when a bioinformatician is closer to the biology he/she is studying, because you can’t do that if you don’t know the biology behind your project.
For example, yesterday I attended a seminar from one of the responsible of Ensembl Compara. My question was: which controls do you use when you update the pipeline to predict orthologs? I was wondering whether, with all the experience in predicting orthologs that the Ensembl Compara programmers have, if they know of any gene for which there is so much literature that anyone can be absolutely sure about its orthologs in other species.
So, what is your favorite question to ask in a seminar of bioinformatics? Which controls are you using in your analysis? 🙂