This is a subjective topic. What is the smartest question you have asked or heard asking in a bioinformatics seminar? Which types of questions to you ask more frequently?
For example, the question that I ask most frequently is 'which are your controls?'. I suspect some people hate me for always asking that :-). What is your favorite question?
I like to ask this delightful question : What are the units on the axes ?
Several replies so far and not one of "why did you write your program in XXX, when YYY would have been better" :->
I jest. I think the smartest questions are based on an actual desire for knowledge as opposed to ones that attempt to boost the ego of the questioner and/or attempt to demean the speaker. Perhaps another question to pose to biostar is "what is the best ego popping reply that you've heard from a speaker".
I digress, some generic questions I ask are whether the is code is free & open source, and if so, where I can get it. If I think the presenter is well versed enough, I'll ask how it compares to other programs in the field. If I want to help I'll ask the more awkward questions privately after the talk.
While I never heard it asked I like the question:
What you’re doing is rather desperate. Wouldn’t you be better off doing some experiments?.
My favourite was: "So just to be clear, all of these software packages are open-source and freely-available elsewhere?"
It was put to the CEO of a bioinformatics company which packaged up free software on a CD and tried to sell it. They even offered the NCBI handbook, "conveniently formatted as a single PDF" for $35.
Known exceptions to your hypothesis please..
Well, I often ask: "Does it work?" and by that I mean "Does it show/represent/display the real biology?"
And I swear the range of answers I've received are really funny. One time someone was showing us this very cool new splice variant display, based on some computational assessment. I said, "Ok. But does it work? Can you show me a sample that shows your display with some well-characterized splice variants from a known gene?"
The answer (I kid you not): "I don't know."
My favourite question when analysis results are presented with nary a word on the procedural intricacies is : Did "YOU" really do this? (Of course, I dont ask that in a seminar, seems preposterous!) Obviously the implication being I would like to meet the smart guy who did these analyses for you, drew your heat maps etc.. and you think R is a letter of the english alphabet.
My favorite question: So you studied Bioinformatics? Well, I have a problem. Do you know the Windows program XYZ? It doesn't work!
"Have you run your code to test for arsenic in the samples?"
What version of Excel did you use?
did you test your model in real life ?
My favorite question is: which are your controls or models? This is because I am curious about how bioinformaticians validate their predictions.
For example, yesterday I attended a seminar from one of the Ensembl Compara developers, and I asked him: which genes do you use as controls when your update your pipeline? I wondered whether there are genes for which there is so much literature that we can be 100% sure of the orthologs in each of the species in Ensembl. I think that the choice of good controls for a pipeline is the moment where a bioinformatician is closer to the biology he/she is studying.
Well, my to question will be based on what kind of bioinformatics seminar it is- Generic or Specific. Though you haven't mentioned the topic of seminar then I will formulate questions totally based on my personal experience.
Specific (Next generation sequencing seminar)
Questions
Generic (Bioiformatics seminar)
Questions
You have done with XXX software/programme, how reliable the software you have used? Have you compared your data with other software/programme?
How do you visualize the data after processing? Anything new here??
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version 2.3.6
+1 .
Yeah, I like this :)