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How do we feel about questions about biological principles that can be confusing to a bioinformatician with no background in biology? While purely biological questions should, I think, be off topic and migrated to Biology, what about questions from bioinformaticians trying to interpret their results?

For example, if someone were to ask about what these weird 0/1 things they see in a VCF file, should we explain what haplotypes and zygosity are? If someone asks about how a PPI network is generated, should we explain ChIP or Y2H methods here?

Basically, how strict is our definition of bioinformatics? This is a subfield of biology, after all.

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  • $\begingroup$ Isn't bioinformatics a subfield of informatics? The question about what is bioinformatics is a though one. BTW +1 $\endgroup$
    – llrs
    Commented May 22, 2017 at 15:29
  • $\begingroup$ @Llopis heh, I admit I may be biased since I come from a background of biology and not computers. I always thought of it as a field of biology and not of informatics. I guess it depends on what you do though. On the other hand, all universities I am familiar with that offer bioinformatics, consider it part of biology and the courses are run by the biology departments. Not that that means much, of course :) $\endgroup$
    – terdon Mod
    Commented May 22, 2017 at 15:31
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    $\begingroup$ The way the word bioinformatics is used these days pretty much suggests any part of biology that involves the use of computers to process data. Once upon a time bioinformatics dealt with the best ways to organised, store, and cross-reference biological data. It was fair to call it subfield of informatics. But most bioinformatician these days wouldn't know the first thing about databases, and as commonly used, itis a subfield of biology. $\endgroup$
    – Ian Sudbery
    Commented May 22, 2017 at 23:11
  • $\begingroup$ @IanSudbery when/where was this? My first contact with the term was in 2001 or so as an undergraduate and then it already meant "any application of computers to answer biological questions". I know some people used "computational biology" for that, and "bioinformatics" for developing tools etc, but I only came across that term more than 10 years later while doing my post doc. $\endgroup$
    – terdon Mod
    Commented May 29, 2017 at 16:33

2 Answers 2

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I think we should indeed explain biological concepts as long as those are clearly relevant to the work of a bioinformatician. So, a general question about transcription should be off topic, but a question about the biological interpretation of computational data (blast output, for example) should be allowed.

A simple example would be a question about interpreting a sequence alignment. While it may look like bioinformatics, it is very hard to interpret such alignments usefully without some basic knowledge about the biological concepts of sequence evolution, the chemical properties of amino acids, protein domains, exons, introns etc. So a good answer would have to include at least some "pure" biology.

I think it will be very hard to set out specific guidelines for this so early in the site's life, but perhaps this is something to bear in mind going forward. I expect that in the following weeks we will start getting such borderline questions and I hope we can get to a consensus about them using real examples.

In the meantime, I propose that as a rule of thumb, we should allow any questions that arise from bioinformatic analyses. If it turns out those are too permissive and too "wet", we can reassess.

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I think that biology questions should be accepted (those relevant to a bioinformatician, as @terdon mentioned).

Bioinformatics is a combination of biology, computer science, and statistics. People with specialisation in one of those areas have a "ground knowledge" and would tend to treat questions as simple that people coming from other areas would find difficult. I don't think it's a good idea to expect that visitors to this site will have expert knowledge in all three areas.

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