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Some general recommendations on master theses are:

a master thesis should be readable without looking up external references

a master thesis should present the topic in a way a someone with a bachelor can understand it

Based on these, I want to have a background chapter which explains particular concepts individually, out of context of the thesis problem. The reader would skip any topic they feel knowledgeable about in this chapter with the confidence that parts of the thesis problem was not skipped when they did so, because the chapter was free-standing.

I feel operating-system internals and malware analysis are not common knowledge, but I don't want to talk about them more than necessary, only the relevant parts. I could weave this into the main text, but I feel it would make it harder to read for both the inexperienced reader and also the experienced reader if at every turn I have to explain other concepts.

My advisor has allowed me to make such a chapter, but I haven’t seen any free-standing background chapters like this in any other papers. What is the consensus?

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I don't know if there is a broad consensus but I have seen background chapters in several papers I read recently in my field (computer engineering). If you have the space to spare (I guess a master thesis will not have a strict page limit?), this seems perfectly reasonable. Make sure to only describe things that are relevant to your research, and highlight/foreshadow how they will matter to the rest of the paper. This will also help clearly demarcate your own contribution from prior work.

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  • I want the chapter to be free-standing, that's why I'm asking. If I removed it completely it should have exactly 0% effect on the paper. The reader would instead be forced to look up all the concepts they don't already know, which would probably be frustrating. The chapter is meant to be skipped over for the experienced reader, so I don't want anything to do with the research question in there. What I'm suggesting is different from the typical literature background chapter. – Mikubyte Apr 6 '17 at 11:35
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    I don't see how these two goals are contradictory. For the background chapter to be removable, the other chapters can't rely on it - but that doesn't mean that in return you have to pretend within that chapter that the rest of the paper doesn't exist. Usually you can give readers a general idea of why you are bothering to teach them this subject. Something like "this resource is managed by this function in this way so if we manage to interfere with this it would present an attack surface" and then in a later chapter you talk about how you actually managed to interfere. – nengel Apr 7 '17 at 17:11
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I think it's fine and normal (and can be done in a Ph.D. thesis as well).

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