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We have got a nice question about PyMol with some upvotes already.

I just wasn't sure whether these questions belong to our community. It is clear to me that the probability of spotting a person who has some experience with particularly this software is higher among biologists, but in my opinion this is not what we would like the site to evolve into.

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I think we should allow this kind of questions, similar to StackOverflow allowing questions about programming tools.

I'd allow questions about usage of biological tools, though programming should still be off-topic. The usual restriction applies, the tools should be something specific to Biology, so questions about your favorite text editor are still off-topic.

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I agree with @biocs and @Mad Scientist in that software should be allowed, but explicit programming questions should be off-topic. I would like to add to this discussion that the end goal must have a biological goal in mind, because I can think of many software suites (eg, Matlab, ImageJ) that can be used for biological applications as much as engineering applications.

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This question is of the same category as those asking for help with experiments like "How can I produce milligram quantities of an isotope-labeled DNA oligomer?". (Just because they don't have a pipette in hand doesn't mean they aren't biologists.) They should be on-topic for Biology as much as the questions asking for biological results.

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