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I know there is biostar, which is specific to bioinformatics questions. However, I feel that there are quite a few parts of bioinformatics that have a lot of biological relevance. Perhaps we should draw the line at programming related questions?

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I'd consider questions about theoretical models using in bioinformatics or about the usage of bioinformatics tools on-topic. All the bioinformatics methods are just additional tools for a biologist, whether its performing a BLAST search or predicting your RNA secondary structure.

We should allow all questions that are asked from a biologists point of view, those are relevant to the users on this site and we should have the expertise to answer them. This would include using bioinformatics tools and understanding the principles behind those tools.

Questions that are about programming should be off-topic, that would stretch the topic of this site a bit too far. The pure programming questions would be on-topic on StackOverflow, while question about the concepts behind the program would be welcome here.

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    $\begingroup$ I completely agree with you and I think it's a very reasonable path to take. Especially since it looks like biostar is going to move out of the SE network and that the bioinformatics proposal will never make it. $\endgroup$ – GWW Dec 15 '11 at 18:19
  • $\begingroup$ @GWW Biostar was never inside in fact... $\endgroup$ – user59 Dec 16 '11 at 13:40
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It depends on the question. A question about the Biology part of bioinformatics is absolutely on-topic. Questions about the computational aspects, or statistical aspects, or programming aspects, are better handled on other sites.

Honestly though, I think this will be the answer for every single "Should Field X related questions be considered off-topic?"

Epidemiology: Biological questions? On-topic. Medical questions? Likely off-topic. Analysis questions? Off-topic. Some questions about the implications of this results? On-topic.

Ecology: Probably mostly on-topic. But questions about the mathematical dynamics of a predator-prey model, when what you're actually talking about is the math? Off-topic. Statistics questions? Off-topic. Questions about how to program some particular Ecology model? Off-topic.

etc. etc. ad infinitum

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