user66: 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.

user112: 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. 

user-1: 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.

user6: 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.

66: <p>We have got <a href="https://biology.stackexchange.com/questions/732/how-do-i-get-the-current-camera-position-in-pymol-so-i-can-reuse-it-in-scripts">a nice question about PyMol</a> with some upvotes already. </p>

<p>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.</p>
 112: <p>This question is of the same category as those asking for help with experiments like "<a href="https://biology.stackexchange.com/q/117/112">How can I produce milligram quantities of an isotope-labeled DNA oligomer?</a>". (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. </p>
 -1: <p>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.</p>
 6: <p>I think we should allow this kind of questions, similar to StackOverflow allowing questions about programming tools. </p>

<p>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.</p>
