The Best Question To Ask In A Bioinformatics Seminar
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11.0 years ago

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?

subjective • 8.5k views
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brentp 23k

"Where can I get the source-code?"

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+1 .

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Yeah, I like this :)

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Bilouweb ★ 1.1k

I like to ask this delightful question : What are the units on the axes ?

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i second that..

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11.0 years ago

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.

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10
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11.0 years ago

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?.

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:-) wonder if there are person doing wet biology who faced the opposite situation.

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Something like: Since you'll NEVER collect enough samples to even get a beginning of an answer to your research question... Wouldn't you be better off running some simulations? If it weren't so mean, it would actually be fun to ask :P

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Neilfws 49k

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.

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Prateek ★ 1.0k

Known exceptions to your hypothesis please..

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Mary 11k

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."

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jvijai ★ 1.2k

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.

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11.0 years ago
Google ▴ 50

My favorite question: So you studied Bioinformatics? Well, I have a problem. Do you know the Windows program XYZ? It doesn't work!

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11.0 years ago

"Have you run your code to test for arsenic in the samples?"

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Made me laugh - thanks Egon :)

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What version of Excel did you use?

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You are a bad man.

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Mike ▴ 40
  • What's about reproducibility of the results (when using random data)?
  • Too low number of test cases.
  • Your tests are biased.
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Well, I DID run 10000 in silico simulations... how many time have YOU replicated your biological experiments?

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11.0 years ago

did you test your model in real life ?

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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.

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And... what answer did you get? Just curious!

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Thaman ★ 3.3k

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

  • Enchancement and technological changes in third generation sequencing. What Equipments, Statistical and computational approaches, and pacakges associated with it.
  • How analysis, test and hypothesis are formulated

Generic (Bioiformatics seminar)

Questions

  • What are the most important tools that Bioinformatician must learn.
  • Programming approaches and trends.
  • How to keep up to date with the trends?
  • References, Journals, blogs, citation and discussion groups
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9.2 years ago
jackuser1979 ▴ 880

You have done with XXX software/programme, how reliable the software you have used? Have you compared your data with other software/programme?

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9.1 years ago
k.nirmalraman ★ 1.1k

How do you visualize the data after processing? Anything new here??

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