Question: The Best Question To Ask In A Bioinformatics Seminar
12
gravatar for Giovanni M Dall'Olio
7.5 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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 • 5.6k views
ADD COMMENTlink modified 7.4 years ago by k.nirmalraman910 • written 7.5 years ago by Giovanni M Dall'Olio26k
22
gravatar for brentp
7.5 years ago by
brentp22k
Salt Lake City, UT
brentp22k wrote:

"Where can I get the source-code?"

ADD COMMENTlink written 7.5 years ago by brentp22k
2

+1 .

ADD REPLYlink written 7.5 years ago by Pierre Lindenbaum108k
1

Yeah, I like this :)

ADD REPLYlink written 7.5 years ago by Thaman3.2k
12
gravatar for Bilouweb
7.5 years ago by
Bilouweb1.1k
Saclay, France
Bilouweb1.1k wrote:

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

ADD COMMENTlink written 7.5 years ago by Bilouweb1.1k
3

http://xkcd.com/833/

ADD REPLYlink written 7.5 years ago by Daniel Swan13k

i second that..

ADD REPLYlink written 7.5 years ago by Prateek1000
11
gravatar for Alastair Kerr
7.5 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

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.

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Alastair Kerr5.2k
10
gravatar for Istvan Albert
7.5 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

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?.

ADD COMMENTlink written 7.5 years ago by Istvan Albert ♦♦ 77k
2

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

ADD REPLYlink written 7.5 years ago by Giovanni M Dall'Olio26k
2

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

ADD REPLYlink written 7.5 years ago by Eric Normandeau9.8k
10
gravatar for Neilfws
7.5 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 7.5 years ago by Neilfws48k
7
gravatar for Prateek
7.5 years ago by
Prateek1000
Boston, MA
Prateek1000 wrote:

Known exceptions to your hypothesis please..

ADD COMMENTlink written 7.5 years ago by Prateek1000
7
gravatar for Mary
7.5 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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."

ADD COMMENTlink written 7.5 years ago by Mary11k
5
gravatar for jvijai
7.5 years ago by
jvijai1.1k
United States
jvijai1.1k wrote:

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.

ADD COMMENTlink written 7.5 years ago by jvijai1.1k
5
gravatar for Google
7.5 years ago by
Google50
Google50 wrote:

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

ADD COMMENTlink written 7.5 years ago by Google50
5
gravatar for Egon Willighagen
7.5 years ago by
Maastricht
Egon Willighagen5.2k wrote:

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

ADD COMMENTlink written 7.5 years ago by Egon Willighagen5.2k
1

Made me laugh - thanks Egon :)

ADD REPLYlink written 7.5 years ago by Daniel Swan13k
5
gravatar for Aaronquinlan
7.5 years ago by
Aaronquinlan10k
United States
Aaronquinlan10k wrote:

What version of Excel did you use?

ADD COMMENTlink written 7.5 years ago by Aaronquinlan10k
7

You are a bad man.

ADD REPLYlink written 7.5 years ago by iw9oel_ad6.0k
4
gravatar for Mike
7.5 years ago by
Mike40
Mike40 wrote:
  • What's about reproducibility of the results (when using random data)?
  • Too low number of test cases.
  • Your tests are biased.
ADD COMMENTlink written 7.5 years ago by Mike40
6

Well, I DID run 10000 in silico simulations... how many time have YOU replicated your biological experiments?

ADD REPLYlink written 7.5 years ago by Eric Normandeau9.8k
4
gravatar for Pierre Lindenbaum
7.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum108k wrote:

did you test your model in real life ?

ADD COMMENTlink written 7.5 years ago by Pierre Lindenbaum108k
4
gravatar for Giovanni M Dall'Olio
7.5 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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.

ADD COMMENTlink written 7.5 years ago by Giovanni M Dall'Olio26k

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

ADD REPLYlink written 7.5 years ago by Ajene80
3
gravatar for Thaman
7.5 years ago by
Thaman3.2k
Finland
Thaman3.2k wrote:

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
ADD COMMENTlink written 7.5 years ago by Thaman3.2k
2
gravatar for jackuser1979
5.7 years ago by
jackuser1979850
US
jackuser1979850 wrote:

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

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by jackuser1979850
1
gravatar for k.nirmalraman
5.6 years ago by
k.nirmalraman910
Germany
k.nirmalraman910 wrote:

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

ADD COMMENTlink written 5.6 years ago by k.nirmalraman910
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